From 7ed99716cf39e955d869a4772617f6496bd545f0 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Fri, 22 Dec 2023 18:45:17 +0100 Subject: [PATCH 01/42] docs: expand workflow description --- README.md | 68 ++++++++++++++++++++++++++++++++++++++----------------- 1 file changed, 47 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 12b3932..370b466 100644 --- a/README.md +++ b/README.md @@ -159,7 +159,7 @@ tested, you can go ahead and run the workflow on your samples. It is suggested to have all the input files for a given run (or hard links pointing to them) inside a dedicated directory, for instance under the _MIRFLOWZ_ root directory. This way, it is easier to keep the data together, -reproduce an analysis and set up Singularity access to them. +reproduce analysis and set up Singularity access to them. #### 1. Prepare a sample table @@ -220,7 +220,7 @@ We recommend creating a copy of the ```bash cp config/config_template.yaml path/to/config.yaml -``` So on that PR I could move this information in the section/file all of this will be written. +``` Open the new copy in your editor of choice and adjust the configuration parameters to your liking. The template explains what each of the @@ -260,9 +260,7 @@ intermediate files generated during the process. The final outputs comprise: 1. A SAM file containing alignments intersecting a pri-miR locus. These alignments intersect with extended start and/or end positions specified in the provided pri-miR annotations. Please note that they may not contribute to the -final counting and may not appear in the final table. Alignments are discarded -if their start and/or end positions differ from the ends of the provided -pri-miR annotations by more bases than the extension used. +final counting and may not appear in the final table. 2. A SAM file containing alignments intersecting a mature miRNA locus. Similar to the previous file, these alignments intersect with extended start and/or end @@ -313,19 +311,45 @@ snakemake \ ## Workflow description -The _MIRFLOWZ_ workflow first processes and indexes the user-provided genome -resources. Afterwards, the user-provided short read small-RNA-seq libraries will -be aligned separately against the genome and transcriptome. For increased -fidelity, two separated aligners, [Segemehl][segemehl] and our in-house tool -[Oligomap][oligomap], are used. All the resulting alignments are merged such -that only the best alignments of each read are kept (smallest edit distance). -Finally, alignments are intersected with the user-provided, pre-processed -miRNA annotation file using [BEDTools][bedtools]. Counts are tabulated -separately for reads consistent with either miRNA precursors, mature miRNA -and/or isomiRs. - -> **NOTE:** For a detailed description of each rule, please, refer to the -> [workflow documentation](pipeline_documentation.md) +The _MIRFLOWZ_ workflow initially processes and indexes the genome resources +provided by the user. The regions corresponding to mature miRNAs are extended +on both sides to accommodate isomiR species with shifted start and/or end +positions. If necessary, pri-miR loci are similarly extended to adjust to the +new miRNA coordinates. + +Subsequently, the user-provided short-read small RNA-seq libraries undergo +quality filtering if a FASTQ file is provided. Alternatively, adapters are +directly removed. The resulting reads are independently mapped to both the +genome and the transcriptome using two distinct aligners: [Segemehl][segemehl] +and our in-house tool [Oligomap][oligomap]. After the mapping, only the best +alignments for each read, determined by the smallest edit distance, are +retained by merging and filtering the resulting alignments into a single file. + +The collection of resulting alignments is then reduced to contain only unique +entries. Due to the short length of the reads and the sequence similarity among +miRNAs, the number of alignments can be high. Therefore, reads aligned beyond a +specified threshold are discarded. To address multimapping, alignments with the +fewest indels are preserved. These alignments are subsequently intersected with +the user-provided, pre-processed miRNA annotation files using +[BEDTools][bedtools]. Note that an alignment will not contribute to the final +count if its start and/or end positions differ significantly from the provided +miRNA annotations, beyond the extension applied to the mature miRNA start +and/or end positions, or by 1 if no extension was applied. Conversely, a +retained read contributes 1/n to all the annotated miRNA species it aligns +with, where `n` is the number of genomic and/or transcriptomic loci it aligns +to. + +_MIRFLOWZ_ employs an unambiguous notation to classify isomiRs using the format +`miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and `3p-shift` +represent the differences between the annotated mature miRNA start and end +positions and those of the alignment, respectively. + +Finally, counts are tabulated separately for reads consistent with either +miRNA precursors, mature miRNA and/or isomiRs and all library counts are +fused into a single table. + +> **NOTE:** For a detailed description of each rule along with some examples, +> please, refer to the [workflow documentation](pipeline_documentation.md). The schema below is a visual representation of the individual workflow steps and how they are related: @@ -337,8 +361,8 @@ and how they are related: _MIRFLOWZ_ is an open-source project which relies on community contributions. You are welcome to participate by submitting bug reports or feature requests, taking part in discussions, or proposing fixes and other code changes. Please -refer to the [contributing guidelines](CONTRIBUTING.md) if you are interested in -contribute. +refer to the [contributing guidelines](CONTRIBUTING.md) if you are interested +in contribute. ## License @@ -346,7 +370,9 @@ This project is covered by the [MIT License](LICENSE). ## Contact -For questions or suggestions regarding the code, please use the [issue tracker][issue-tracker]. Do not hesitate on contacting us via [email][email] for any other inquiries. +For questions or suggestions regarding the code, please use the +[issue tracker][issue-tracker]. Do not hesitate on contacting us via +[email][email] for any other inquiries. © 2023 [Zavolab, Biozentrum, University of Basel][zavolab] From ecc920ca8846bd1d4bf2733f4bd37f46822883ed Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 24 Dec 2023 13:56:49 +0100 Subject: [PATCH 02/42] docs: expand rule descriptions --- pipeline_documentation.md | 637 ++++++++++++++++++++++++++------------ 1 file changed, 431 insertions(+), 206 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index a3f50ba..b713244 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -79,6 +79,7 @@ on installation and usage please see [here](README.md). - [`sort_uncollapse_reads_bam_by_position`](#sort_uncollapse_reads_bam_by_position) - [`index_uncollapse_reads_bam`](#index_uncollapse_reads_bam) + ## Third-party software used @@ -99,13 +100,13 @@ on installation and usage please see [here](README.md). ## Description of workflow steps > The workflow consists of four Snakemake files: A main `Snakefile` and an -individual Snakemake file for each step in the workflow (the file preparation, -the reads mapping and the miRNA quantification). The main `Snakefile` contains -the configuration file validation along with the inclusion of the -sub-workflows. Individual steps of the workflow are described briefly, and -links to the respective software manuals are given. Parameters that can be -modified by the user (via the samples table and the configuration file) are -also described. +> individual Snakemake file for each step in the workflow (the genome resources +> preparation, the reads mapping and the miRNA quantification). The main +> `Snakefile` contains the configuration file validation along with the +> inclusion of the sub-workflows. Individual steps of the workflow are +> described briefly along with some examples, and links to the respective +> software manuals are given. Parameters that can be modified by the user (via +> the samples table and the configuration file) are also described. ### Rule graph @@ -127,10 +128,11 @@ Visual representation of the workflow. Automatically prepared with Parameter name | Description | Data type(s) --- | --- | --- -sample | Descriptive sample name. | `str` -sample_file | Path of the library file in either `.fa.gz` or `.fastq.gz` format. | `str` -adapter | Required for [Cutadapt](#third-party-software-used). Use a value such as `XXXXXXXXXX` if no adapter is present or if no trimming is desired | `str` -format | There are two allowed values, `fa` and `fastq` according to the library format | `str` +sample | Arbitrary name for the miRNA sequence library. | `str` +sample_file | Path to the `gzip`ped miRNA sequencing library file. The path must be relative to the directory where the workflow will be run. | `str` +adapter | Sequence of the 3'-end adapter used during library preparation. Required for [Cutadapt](#third-party-software-used). Use a value such as `XXXXXXXXXX` if no adapter is present or if no trimming is desired | `str` +format | One of `fa`/`fasta` or `fq`/`fastq`, if the library file is in FASTA or FASTQ format, respectively. + | `str` #### Configuration file @@ -148,17 +150,15 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - pri-miR intersections file (`.bed`); from - [**intersect_extended_primir**](#intersect_extended_primir) - - miRNA intersections file (`.bed`); from - [**intersect_extended_mirna**](#intersect_extended_mirna) - - Alignments file, sorted and tagged (`.sam`); from - [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - - (iso)miR and/or pri-miR counts table (`.tab`); from + - (Workflow output) SAM file with the pri-miR intersecting alignments; from + [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) + - (Workflow output) SAM file with the mature miRNA intersecting alignments; from + [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) + - (Workflow output) (iso)miR and/or pri-miR counts table (`.tab`); from [**merge_tables**](#merge_tables) - - Alignments file (`.bam`); from + - (Workflow output) BAM file with the contributing alignments, sorted; from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - `BAM` index file (`.bam.bai`); from + - (Workflow output) BAM index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) @@ -177,13 +177,13 @@ Target rule as required by [Snakemake][docs-snakemake]. [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome) - Exon annotations (`.bed`); from [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) - - Genome header (`.sam`); from + - SAM header (`.sam`); from [**create_genome_header**](#create_genome_header) - Tab-separated table mapping chromosome name(s) and length(s) (`.tsv`); from [**extract_chr_len**](#extract_chr_len) - - Primary miRNA transcript (pri-miR) extended annotation (`.gff3`); + - Primary miRNA transcript (pri-miR) extended annotations (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) - - Mature miRNA (miRNA) extended annotation (`.gff3`); + - Mature miRNA (miRNA) extended annotations (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) @@ -192,9 +192,9 @@ Target rule as required by [Snakemake][docs-snakemake]. Trim genome sequence IDs with a [**custom script**][custom-script-trim-id]. - **Input** - - Genome sequence file (`.fasta`) + - (Workflow input) Genome sequence, `gzip`ed (`.fa.gz`/`.fasta.gz`) - **Output** - - Genome sequence file, trimmed IDs (`.fasta`); used in + - Genome sequence, trimmed IDs (`.fa`); used in [**extract_transcriptome_seqs**](#extract_transcriptome_seqs), [**create_genome_header**](#create_genome_header), [**create_index_genome_fasta**](#create_index_genome), @@ -205,25 +205,28 @@ Trim genome sequence IDs with a [**custom script**][custom-script-trim-id]. #### `extract_transcriptome_seqs` -Create transcriptome from genome and genome annotations with +Create transcriptome from genome sequence and annotations with [**cufflinks**](#third-party-software-used). - **Input** - - Genome sequence file (`.fasta`) - - Genome annotation file (.`gtf`) + - Genome sequence, trimmed IDs (`.fa`); from + [**trim_genome_seq_ids**](#trim_genome_seq_ids) + - (Workflow input) Genome annotations, `gzip`ed (`.gtf.gz`) - **Output** - - Transcriptome sequence file (`.fasta`); used in + - Transcriptome sequence (`.fa`); used in [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) #### `trim_transcriptome_seq_ids` -Trim transcriptome sequence IDs with a [**custom script**][custom-script-trim-id]. +Trim transcriptome sequence IDs with a +[**custom script**][custom-script-trim-id]. - **Input** - - Transcriptome sequence file (`.fasta`) + - Transcriptome sequence (`.fa`); from + [**extract_transcriptome_seqs**](#extract_transcriptome_seqs) - **Output** - - Transcriptome sequence, trimmed IDs (`.fasta`); used in + - Transcriptome sequence, trimmed IDs (`.fa`); used in [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome), [**mapping_transcriptome_segemehl**](#mapping_transcriptome_segemehl) and [**mapping_transcriptome_oligomap**](#mapping_transcriptome_oligomap) @@ -235,10 +238,10 @@ Generate transcriptome index for [**segemehl**](#third-party-software-used) short read aligner. > The transcriptome index only needs to be generated once for each combination -of genome and annotations and sample sets. +> of genome and annotations and sample sets. - **Input** - - Transcriptome sequence file, trimmed IDs (`.fasta`); from + - Transcriptome sequence, trimmed IDs (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - **Output** - segemehl transcriptome index (`.idx`); used in @@ -251,10 +254,10 @@ Generate genome index for [**segemehl**](#third-party-software-used) short read aligner. > The genome index only needs to be generated once for each combination -of annotations and sample sets. +> of annotations and sample sets. - **Input** - - Genome sequence file with trim IDs (`.fasta`); from + - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - segemehl genome index (`.idx`); used in @@ -267,7 +270,7 @@ Retrieve exon annotations from genome annotations with a [**custom script**][custom-script-get-lines]. - **Input** - - Genomic annotations (`.gtf`) + - (Workflow input) Genome annotations, `gzip`ed (`.gtf.gz`) - **Output** - Exon annotations (`.gtf`); used in [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) @@ -286,45 +289,46 @@ Convert exon annotations `.gtf` to `.bed` with a #### `create_genome_header` -Create `SAM` header for the genome with +Create SAM header for the genome with [**SAMtools**](#third-party-software-used). -> Required by [SAMtools](#third-party-software-used) to work with the alignment -file. +> Required by [SAMtools](#third-party-software-used) to work with the +> alignments file. - **Input** - - Genome sequence file, trimmed IDs (`.fasta`); from + - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - Genome header (`.sam`); used in [add_header_all_maps](#add_header_all_maps) + - SAM genome header (`.sam`); used in + [add_header_all_maps](#add_header_all_maps) #### `map_chr_names` -Map UCSC-like chromosome names with Ensembl-like ones in miRNA annotation +Map UCSC-like chromosome names with Ensembl-like ones in miRNA annotations with a [**custom script**][custom-script-map-chr]. > Required by [BEDTools](#third-party-software) to intersect alignments with -miRNA annotations. Several mapping tables are available [here][chr-maps]. +> miRNA annotations. Several mapping tables are available [here][chr-maps]. - **Input** - - miRNA annotations (`.gff3`) - - Tab-separated mappings table (`.tsv`) + - (Workflow input) miRNA annotations (`.gff3`) + - (Workflow input) Tab-separated chromosome name mappings table (`.tsv`) - **Output** - - miRNA annotations with mapped genes(`.gff3`); used in + - miRNA annotations, mapped chromosome name(s) (`.gff3`); used in [**extend_mirs_annotations**](#extend_mirs_annotations) #### `create_index_genome_fasta` -Create a `FASTA` index for the genome with +Create a FASTA index for the genome with [**SAMtools**](#third-party-software-used). - **Input** - - Genome sequence file, trimmed IDs (`.fasta`); from + - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - `FASTA` genome index (`.fa.fai`); used in + - FASTA genome index (`.fa.fai`); used in [**extract_chr_len**](#extract_chr_len) @@ -333,7 +337,7 @@ Create a `FASTA` index for the genome with Extract chromosome(s) length from the genome sequence. - **Input** - - `FASTA` genome index (`.fa.fai`); from + - FASTA genome index (`.fa.fai`); from [**create_index_genome_fasta**](#create_index_genome_fasta) - **Output** - Tab-separated table mapping chromosome name(s) and length(s) (`.tsv`); used @@ -346,22 +350,76 @@ Extend miRNA annotations and split the file by feature with a [**custom script**][custom-script-mir-ext]. > Mature miRNA regions are extended on both sides to account for isomiR species -with shifted start and/or end positions. If required, pri-miR loci are also -extended to accommodate the new miRNA coordinates. +> with shifted start and/or end positions without exceeding chromosome(s) +> boundaries. If required, pri-miR loci are also extended to accommodate the +> new miRNA coordinates. In addition, pri-miR names are modified to record the +> final positions by appending `_-y` and `_+x` to it, where `y` is the 5' +> shift and `x` the 3' shift. - **Input** - - miRNA annotations with mapped chromosomes(`.gff3`); from + - miRNA annotations, mapped chromosome name(s) (`.gff3`); from [**map_chr_names**](#map_chr_names) - **Parameters** - **config_template.yaml** - `extension`: Number of nucleotides by which mature miRNA annotated - regions are extended (default 6) + regions are extended at most (default: 6) - **Output** - - Primary miRNA transcript (pri-miR) extended annotation (`.gff3`); used in + - Primary miRNA transcript (pri-miR) extended annotations (`.gff3`); used in [**intersect_extended_primir**](#intersect_extended_primir) - - Mature miRNA (miRNA) extended annotation (`.gff3`); used in + - Mature miRNA (miRNA) extended annotations (`.gff3`); used in [**intersect_extended_mirna**](#intersect_extended_mirna) +- **Examples** + +```console +Example 1 | Mature miRNA extension + +IN: + pri-miR entry: + 19 . miRNA_primary_transcript 2517 2614 . + . ID=MI0003141;Alias=MI0003141;Name=hsa-mir-512-2 + mature miRNA entry: + 19 . miRNA 2536 2558 . + . ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003141 + extension: + 6 +OUT: + pri-miR entry: + 19 . miRNA_primary_transcript 2517 2614 . + . ID=MI0003141;Alias=MI0003141;Name=hsa-mir-512-2_-0_+0 + mature miRNA entry: + 19 . miRNA 2530 2564 . + . ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003141 + + +Example 2 | Mature miRNA and pri-miR extension + +IN: + pri-miR entry: + 19 . miRNA_primary_transcript 9 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1 + mature miRNA entry: + 19 . miRNA 12 74 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 + extension: + 6 +OUT: + pri-miR entry: + 19 . miRNA_primary_transcript 6 124 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-3_+2 + mature miRNA entry: + 19 . miRNA 6 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 + + +Example 3 | Matrue miRNA exceeding chromosome boundaries extension + +IN: + pri-miR entry: + 19 . miRNA_primary_transcript 2 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1 + mature miRNA entry: + 19 . miRNA 3 74 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 + extension: + 6 +OUT: + pri-miR entry: + 19 . miRNA_primary_transcript 0 124 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-2_+2 + mature miRNA entry: + 19 . miRNA 0 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 +``` + ### Map workflow #### `finish_map` @@ -371,65 +429,67 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - `BAM` index file (`.bam.bai`); from + - BAM index (`.bam.bai`); from [**index_all_alns_bam**](#index_all_alns_bam) - - #### `start` Copy and rename read files. > Local rule. -Depending on the read files format, the output files undergo a quality filter -(`.fastq`) or are directly formatted (`.fa`). +> Depending on the library file format, the output file undergoes a quality +> filter (`.fastq`) or is directly formatted (`.fa`). - **Input** - - Reads file (`.fa.gz`, `.fastq.gz`) + - (Workflow input) miRNA sequencing library, `gzip`ed + (`.fa.gz`/`.fasta.gz` or `.fq.gz`/`.fastq.gz`) - **Output** - - Reads file, copied, renamed (`.fa`, `.fastq`); used in - [**fastq_quality_filter**](#fastq_quality_filter) or + - miRNA sequencing library, copied, renamed (`.fa`, `.fastq`); used in + [**fastq_quality_filter**](#fastq_quality_filter) and/or [**format_fasta**](#format_fasta) #### `fastq_quality_filter` -Conduct quality control for reads library with +Conduct quality control for reads library with [**fastx_toolkit**](#third-party-software-used). - **Input** - - Reads file, copied, renamed (`.fastq`); from [**start**](#start) + - miRNA sequencing library, copied, renamed (`.fastq`); from + [**start**](#start) - **Parameters** - **config_template.yaml** - - `q_value`: Minimum Q (Phred) score to keep (default 10) + - `q_value`: Minimum Q (Phred) score to keep (default: 10) - `p_value`: Minimum % of bases that must have a Q (Phred) quality - (default 50) + (default: 50) - **Output** - - Reads file, filtered (`.fastq`); used in + - miRNA sequencing library, filtered (`.fastq`); used in [**fastq_to_fasta**](#fastq_to_fasta) #### `fastq_to_fasta` -Convert reads file from `.fastq` to `.fa` with +Convert reads file from FASTQ to FASTA with [**fastx_toolkit**](#third-party-software-used). +> Sequence identifiers are renamed to numbers. + - **Input** - - Reads file, filtered (`.fastq`); from + - miRNA sequencing library, filtered (`.fastq`); from [**fastq_quality_filter**](#fastq-quality-filter) - **Output** - - Reads file (`.fa`); used in [**format_fasta**](#format_fasta) + - miRNA sequencing library (`.fa`); used in [**format_fasta**](#format_fasta) #### `format_fasta` -Format reads to appear on a single line with +Format read's sequences to appear on a single line with [**fastx_toolkit**](#third-party-software-used). - **Input** - - Reads file (`.fa`); from [**start**](#start) or + - miRNA sequencing library (`.fa`); from [**start**](#start) or [**fastq_to_fasta**](#fastq_to_fasta) - **Output** - - Reads file, formatted (`.fa`); used in + - miRNA sequencing library, formatted (`.fa`); used in [**remove_adapters**](#remove_adapters) @@ -439,21 +499,22 @@ Trim adapters and `N` bases at either end. Filter reads by minimum length and number of inner `N` bases with [**cutadapt**](#third-party-software-used). - **Input** - - Reads file (`.fa`); from [**format_fasta**](#format_fasta) + - miRNA sequencing library, formatted (`.fa`); from + [**format_fasta**](#format_fasta) - **Parameters** - **samples.tsv** - - Adapter to be removed; specify in sample table column `adapter` + - Adapter to be removed; specified in the sample's table column `adapter` - **config_template.yaml** - `error_rate`: Fraction of allowed errors in the matched adapters - (default 0.1) + (default: 0.1) - `overlap`: Minimum overlap length between adapter and read to trim the - bases (default 3) + bases (default: 3) - `minimum_length`: Minimum length for a processed read to be kept - (default 15) - - `max_n`: Maximum number of `N` bases for a processed read to be kept - (default 0) + (default: 15) + - `max_n`: Maximum number of `N` bases for a processed read to be kept + (default: 0) - **Output** - - Reads file (`.fa`; used in + - miRNA sequencing library, filtered, without adapters (`.fasta`); used in [**collapse_identical_reads**](#collapse_identical_reads) @@ -462,10 +523,15 @@ number of inner `N` bases with [**cutadapt**](#third-party-software-used). Collapse and rename identical reads [**fastx_toolkit**](#third-party-software-used). +> Sequences are renamed in the format `R-N`, where `R` is the assigned number +> to the unique entry, and `N` is the amount of identical sequences within the +> library collapsed in it. + - **Input** - - Reads file (`.fa`); from [**remove_adapters**](#remove_adapters) + - miRNA sequencing library, filtered, without adapters (`.fasta`); from + [**remove_adapters**](#remove_adapters) - **Output** - - Reads file, collapsed, rename; used in + - miRNA sequencing library, collapsed, renamed (`.fasta`); used in [**filter_fasta_for_oligomap**](#filter_fasta_for_oligomap), [**map_genome_segemehl**](#map_genome_segemehl) and [**map_transcriptome_segemehl**](#map_transcriptome_segemehl) @@ -477,9 +543,9 @@ Align short reads to reference genome with [**segemehl**](#third-party-software-used). - **Input** - - Reads file, collapsed (`.fa`); from + - miRNA sequencing library, collapsed, renamed (`.fasta`); from [**collapse_identical_reads**](#collapse_identical_reads) - - Genome sequence (`.fa`); from + - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - segemehl genome index (`idx`); from [**generate_segemehl_index_genome**](#generate_segemehl_index_genome) @@ -494,9 +560,9 @@ Align short reads to reference transcriptome with [**segemehl**](#third-party-software-used). - **Input** - - Reads file, collapsed (`.fa`); from + - miRNA sequencing library, collapsed (`.fa`); from [**collapse_identical_reads**](#collapse_identical_reads) - - Transcriptome sequence (`.fa`); from + - Transcriptome sequence, trimmed IDs (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - segemehl transcriptome index (`idx`); from [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome) @@ -509,16 +575,21 @@ Align short reads to reference transcriptome with Filter reads by length with a [**custom script**][custom-script-validation]. +> Required for the mapping optimal speed. Oligomap is specifically written for +> short reads. Therefore, reads with more bases than the default maximum (30 +> nts) makes the mapping slower. + - **Input** - - Reads file, collapsed (`.fa`); from + - miRNA sequencing library, collapsed, renamed (`.fasta`); from [**collapse_identical_reads**](#collapse_identical_reads) - **Parameters** - **config_template.yaml** - - `max_length_reads`: Maximum length of processed reads to map with - [**oligomap**](#third-party-software-used) + - `max_length_reads`: Maximum length of processed reads to be mapped with + [**oligomap**](#third-party-software-used) (default: 30) - **Output** - - Reads file (`.fa`); used in [**map_genome_oligomap**](#map_genome_oligomap) - and [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) + - miRNA sequencing library, collapsed, filtered (`.fasta`); used in + [**map_genome_oligomap**](#map_genome_oligomap) and + [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) #### `map_genome_oligomap` @@ -526,13 +597,16 @@ Filter reads by length with a [**custom script**][custom-script-validation]. Align short reads to reference genome with [**oligomap**](#third-party-software-used). +> Refer to Oligomap's [**Output format section**][oligomap-out] for a specific +> explanation and examples on the output format. + - **Input** - - Reads file, collapsed (`.fa`); from + - miRNA sequencing library, collapsed, filtered (`.fasta`); from [**filter_fasta_for_oligomap**](#filter_fasta_for_oligomap) - - Genome sequence (`.fa`); from + - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - Alignments file (`.fa`); used in + - Alignments file (`.fasta`); used in [**sort_genome_oligomap**](#sort_genome_oligomap) - Alignment report (`.txt`); used in [**sort_genome_oligomap**](#sort_genome_oligomap) @@ -544,32 +618,33 @@ Sort [**oligomap**](#third-party-software-used) alignments by query name with a [**custom script**][custom-script-blocksort]. - **Input** - - Alignments file (`.fa`); from + - Alignments file (`.fasta`); from [**map_genome_oligomap**](#map_genome_oligomap) - Alignment report (`.txt`); from [**map_genome_oligomap**](#map_genome_oligomap) - **Output** - - Alignments file, sorted (`.fa`); used in - [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) - - Alignment report, sorted (`.txt`); used in + - Alignments file, sorted (`.fasta`); used in [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) #### `convert_genome_to_sam_oligomap` -Convert aligned reads `.fa` to `.sam` and filter alignments by number of hits -with a [**custom script**][custom-script-oligo-sam]. +Convert aligned reads `.fasta` to `.sam` and filter alignments by number of +hits with a [**custom script**][custom-script-oligo-sam]. + +> Given the short length of the reads and the sequence similarity among miRNAs, +> the number of hits can be notably high. Therefore, reads aligned beyond a +> specified value are disregarded. - **Input** - - Alignments file, sorted (`.fa`); from - [**sort_genome_oligomap**](#sort_genome_oligomap) - - Alignment report, sorted (`.txt`); from + - Alignments file, sorted (`.fasta`); from [**sort_genome_oligomap**](#sort_genome_oligomap) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of hits an alignment can have to be kept + - `nh`: Maximum number of mappings per read to be kept (default: 100) - **Output** - - Alignments file (`.sam`); used in [**merge_genome_maps**](#merge_genome_maps) + - Alignments file, filtered (`.sam`); used in + [**merge_genome_maps**](#merge_genome_maps) #### `map_transcriptome_oligomap` @@ -577,13 +652,16 @@ with a [**custom script**][custom-script-oligo-sam]. Align short reads to reference transcriptome with [**oligomap**](#third-party-software-used). +> Refer to Oligomap's [Output format section][oligomap-out] for a specific +> explanation and examples on the output format. + - **Input** - - Reads file (`.fa`); from + - miRNA sequencing library, collapsed, filtered (`.fasta`); from [**filter_fasta_for_oligomap**](#filter_fasta_for_oligomap) - - Transcriptome sequence (`.fa`); from + - Transcriptome sequence, trimmed IDs (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - **Output** - - Alignments file (`.fa`); used in + - Alignments file (`.fasta`); used in [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - Alignment report (`.txt`); used in [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) @@ -595,32 +673,32 @@ Sort [**oligomap**](#third-party-software-used) alignments by query name with a [**custom script**][custom-script-blocksort]. - **Input** - - Alignments file (`.fa`); from + - Alignments file (`.fasta`); from [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) - Alignment report (`.txt`); from [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) - **Output** - - Aligned file, sorted (`.fa`); used in + - Alignments file, sorted (`.fasta`); used in [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptome_to_sam_oligomap) - - Alignment report, sorted (`.txt`); used in - [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptme_to_sam_oligomap) #### `convert_transcriptome_to_sam_oligomap` -Convert aligned reads `.fa` to `.sam` and filter alignments by number of hits -with a [**custom script**][custom-script-oligo-sam]. +Convert aligned reads `.fasta` to `.sam` and filter alignments by number of +hits with a [**custom script**][custom-script-oligo-sam]. + +> Given the short length of the reads and the sequence similarity among miRNAs, +> the number of hits can be notably high. Therefore, reads aligned beyond a +> specified value are disregarded. - **Input** - - Alignments file, sorted (`.fa`); from - [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - - Alignment report, sorted (`.txt`); from + - Alignments file, sorted (`.fasta`); from [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of hits an alignment can have to be kept + - `nh`: Maximum number of mappings per read to be kept (default: 100) - **Output** - - Alignments file (`.sam`); used in + - Alignments file, filtered (`.sam`); used in [**merge_transcriptome_maps**](#merge_transcriptome_maps) @@ -632,7 +710,7 @@ Concatenate [**segemehl**](#third-party-software-used) and - **Input** - Alignments file (`.sam`); from [**map_genome_segemehl**](#map_genome_segemehl) - - Alignments file (`.sam`); from + - Alignments file, filtered (`.sam`); from [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) - **Output** - Alignments file (`.sam`); used in @@ -647,7 +725,7 @@ Concatenate [**segemehl**](#third-party-software-used) and - **Input** - Alignments file (`.sam`); from [**map_transcriptome_segemehl**](#map_transcriptome_segemehl) - - Alignments file (`.sam`); from + - Alignments file, filtered (`.sam`); from [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptome_to_sam_oligomap) - **Output** - Alignments file (`.sam`); used in @@ -659,12 +737,17 @@ Concatenate [**segemehl**](#third-party-software-used) and Filter merged genome alignments by the number of hits with a [**custom script**][custom-script-nh-filter]. +> Given the short length of the reads, the sequence similarity among miRNAs, +> and the merging of two different mapping results, the number of hits can +> be notably high. Therefore, reads aligned beyond a specified value are +> disregarded. + - **Input** - Alignments file (`.sam`); from [**merge_genome_maps**](#merge_genome_maps) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of mappings per read to be kept (default 100) + - `nh`: Maximum number of mappings per read to be kept (default: 100) - **Output** - Alignments file, filtered (`.sam`); used in [**remove_header_genome_mappings**](#remove_header_genome_mappings) @@ -674,12 +757,17 @@ Filter merged genome alignments by the number of hits with a Filter merged transcriptome alignments by the number of hits with a [**custom script**][custom-script-nh-filter]. +> Given the short length of the reads, the sequence similarity among miRNAs, +> and the merging of two different mapping results, the number of hits can +> be notably high. Therefore, reads aligned beyond a specified value are +> disregarded. + - **Input** - Alignments file (`.sam`); from [**merge_transcriptome_maps**](#merge_transcriptme_maps) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of mappings per read to be kept (default 100) + - `nh`: Maximum number of mappings per read to be kept (default: 100) - **Output** - Alignments file, filtered (`.sam`); used in [**remove_header_transcriptome_mappings**](#remove_header_transcriptome_mappings) @@ -687,41 +775,43 @@ Filter merged transcriptome alignments by the number of hits with a #### `remove_header_genome_mappings` -Remove the `SAM` header of the genome alignments file with +Remove the SAM header of the genome alignments file with [**SAMtools**](#third-party-software-used). - **Input** - Alignments file (`.sam`); from [**filter_genome_by_nh**](#filter_genome_by_nh) - **Output** - - Alignments file (`.sam`); used in [**merge_all_maps**](#merge_all_maps) + - Alignments file, without SAM header (`.sam`); used in + [**merge_all_maps**](#merge_all_maps) #### `remove_header_transcriptome_mappings` -Remove the `SAM` header of the transcriptome alignments file with +Remove the SAM header of the transcriptome alignments file with [**SAMtools**](#third-party-software-used). - **Input** - Alignments file (`.sam`); from [**filter_transcriptome_by_nh**](#filter_transcriptome_by_nh) - **Output** - - Alignments file (`.sam`); used in + - Alignments file, without SAM header (`.sam`); used in [**transcriptome_to_genome_maps**](#transcriptome_to_genome_maps) #### `transcriptome_to_genome_maps` -Convert the alignments transcriptome coordinates to genomic ones with a +Convert the alignment's transcriptome coordinates to genomic ones with a [**custom script**][custom-script-sam-trx]. - **Input** - - Alignments file (`.sam`); from + - Alignments file, without SAM header (`.sam`); from [**remove_header_transcriptome_mappings**](#remove_header_transcriptome_mappings) - Exon annotations (`.bed`); from [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) - **Output** - - Alignments file (`.sam`); used in [**merge_all_maps**](#merge_all_maps) + - Alignments file, without SAM header (`.sam`); used in + [**merge_all_maps**](#merge_all_maps) #### `merge_all_maps` @@ -729,21 +819,22 @@ Convert the alignments transcriptome coordinates to genomic ones with a Concatenate the four alignments files into a single file. - **Input** - - Alignments file (`.sam`); from + - Alignments files, without SAM header (`.sam`); from [**remove_header_genome_mappings**](#remove_header_genome_mappings) and [**transcriptome_to_genome_maps**](#transcriptome_to_genome_maps) - **Output** - - Alignments file (`.sam`); used in + - Alignments file, without SAM header (`.sam`); used in [**add_header_all_maps**](#add_header_all_maps) #### `add_header_all_maps` -Add the `SAM` header to the aligned reads with +Add the SAM header to the aligned reads merged file with [**SAMtools**](#third-party-software-used). - **Input** - - Alignments file (`.sam`); from [**merge_all_maps**](#merge_all_maps) + - Alignments file, without SAM header (`.sam`); from + [**merge_all_maps**](#merge_all_maps) - **Output** - Alignments file (`.sam`); used in [**sort_maps_by_id**](#sort_maps_by_id) @@ -766,31 +857,94 @@ Remove duplicate and inferior alignments with a [**custom script**][custom-script-remove-dup]. > Alignments are considered to be duplicates if having identical entries for -the fields `QNAME`, `FLAG`, `RNAME`, `POS` and `CIGAR`. -Alignments are considered to be inferiors if having the same `QNAME` and -a bigger edit distance than the minimum one within the group. +> the fields `QNAME`, `FLAG`, `RNAME`, `POS` and `CIGAR`. +> Alignments are considered to be inferiors if having the same `QNAME` and +> a bigger edit distance than the smaller one within the group. The tags `NH` +> (number of hits) and `HI` (query hit index) are updated accordingly. - **Input** - - Alignments file, sorted (`.sam`); from [**sort_maps_by_id**](#sort_maps_by_id) + - Alignments file, sorted (`.sam`); from + [**sort_maps_by_id**](#sort_maps_by_id) - **Output** - - Alignments file (`.sam`); used in + - Alignments file, filtered (`.sam`); used in [**filter_by_indels**](#filter_by_indels) +- **Examples** + +```console +Example 1 | Remove duplicates + +IN: + 1-2 0 19 44414 1 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * HI:i:0 NH:i:1 NM:i:0 MD:Z:21 RG:Z:A1 YZ:Z:0 + 1-2 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * NM:i:0 MD:Z:21 NH:i:1 +OUT: + 1-2 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 + + +Example 2 | Remove inferiors single alignment + +IN: + 1-704 16 19 207362 1 18M * 0 0 CCCGGGCCCGGCGCGCCG * HI:i:0 NH:i:2 NM:i:0 MD:Z:18 RG:Z:A1 YZ:Z:0 + 1-704 272 19 471264 1 16M1I1M * 0 0 CCCGGGCCCGGCGCGCCG * HI:i:1 NH:i:2 NM:i:2 MD:Z:11G5 RG:Z:A1 YZ:Z:0 +OUT: + 1-704 16 19 207362 1 18M * 0 0 CCCGGGCCCGGCGCGCCG * HI:i:0 NH:i:1 NM:i:0 MD:Z:18 RG:Z:A1 YZ:Z:0 + + +Example 3 | Remove inferiors multiple alignments +IN: + + 1-1197 0 19 56327 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:0 NH:i:4 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 + 1-1197 256 19 68983 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:1 NH:i:4 NM:i:3 MD:Z:1C10AT1 RG:Z:A1 YZ:Z:0 + 1-1197 256 19 76967 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:2 NH:i:4 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 + 1-1197 256 19 92363 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:4 NH:i:4 NM:i:3 MD:Z:1C11TA RG:Z:A1 YZ:Z:0 + +OUT: + 1-1197 0 19 56327 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:0 NH:i:2 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 + 1-1197 256 19 76967 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:1 NH:i:2 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 +``` #### `filter_by_indels` -Remove multimappers favoring mismatches over indels with a +Filter multimappers favoring mismatches over indels with a [**custom script**][custom-script-filter-mm]. +> Under the assumption that indels are less frequent than mismatches only +> those alignments (of the same read with the same edit distance) with the +> lowest number of indels are kept. This approach allows the presence of +> multimappers and/or indels after the filtering if the alignments contain the +> same proportion of mismatches vs. indels. + - **Input** - - Alignments file, sorted (`.sam`); from + - Alignments file, sorted, filtered (`.sam`); from [**remove_inferiors**](#remove_inferiors) - **Output** - - Alignments file (`.sam`); used in + - Alignments file, sorted, filtered (`.sam`); used in [**convert_all_alns_sam_to_bam**](#convert_all_alns_sam_to_bam) and [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primr) +- **Examples** + +```console +Example 1 | Different proportion of mismatches vs. indels +IN: + 1-1 16 19 77595 255 14M1D8M * 0 0 GCAGGAGAATCACTGATGTCAG * MD:Z:14^T2A1C3 NH:i:2 NM:i:3 XA:Z:Q XI:i:1 + 1-1 0 19 330456 255 4M1D1M1I3M1D13M * 0 0 CTGACATCAGTGATTCTCCTGC * MD:Z:4^G4^A13 NH:i:2 NM:i:3 XA:Z:Q XI:i:0 +OUT: + 1-1 16 19 77595 255 14M1D8M * 0 0 GCAGGAGAATCACTGATGTCAG * MD:Z:14^T2A1C3 NM:i:3 XA:Z:Q XI:i:1 NH:i:1 HI:i:1 + + +Example 2 | Equal proportion of mismatches vs. indels + +IN: + 1-1 0 19 142777 255 15M1I5M * 0 0 GCTAGGTGGGAGGCTTGAAGC * MD:Z:4C0T14 NH:i:3 NM:i:3 XA:Z:Q XI:i:0 + 1-1 16 19 270081 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14G0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:2 + 1-1 16 19 545543 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14A0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:1 +OUT: + 1-1 0 19 142777 255 15M1I5M * 0 0 GCTAGGTGGGAGGCTTGAAGC * MD:Z:4C0T14 NH:i:3 NM:i:3 XA:Z:Q XI:i:0 + 1-1 16 19 270081 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14G0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:2 + 1-1 16 19 545543 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14A0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:1 +``` #### `convert_all_alns_sam_to_bam` @@ -798,10 +952,10 @@ Convert alignments `.sam` file to `.bam` with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -with pri-miR annotations. +> with pri-miR annotations. - **Input** - - Alignments file (`.sam`); from [**filter_by_indels**](#filter_by_indels) + - Alignments file, filtered (`.sam`); from [**filter_by_indels**](#filter_by_indels) - **Output** - Alignments file (`.bam`); used in [**sort_all_alns_bam_by_position**](#sort_all_alns_bam_by_position) @@ -812,7 +966,7 @@ with pri-miR annotations. Sort alignments by position with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -with pri-miR annotations more efficiently. +> with pri-miR annotations more efficiently. - **Input** - Alignments file (`.bam`); from @@ -825,16 +979,16 @@ with pri-miR annotations more efficiently. #### `index_all_alns_bam` -Create index `BAM` file with [**SAMtools**](#third-party-software-used). +Create index BAM file with [**SAMtools**](#third-party-software-used). > Indexing is required by genome viewers such as IGV to quickly display -alignments in a genomic region of interest. +> alignments in a genomic region of interest. - **Input** - - Alignments file (`.bam`); from + - Alignments file, sorted (`.bam`); from [**sort_all_alns_bam_by_position**](#sort_all_alns_bam_by_position) - **Output** - - `BAM` index file (`.bam.bai`); used in + - BAM index file (`.bam.bai`); used in [**intersect_extended_primir**](#intersect_extended_primir) @@ -851,13 +1005,11 @@ Target rule as required by [Snakemake][docs-snakemake]. [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - - Alignments file, sorted, tagged (`.sam`); from - [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - (iso)miR and/or pri-miR counts table (`.tab`); from [**merge_tables**](#merge_tables) - - Alignments file (`.bam`); from + - Alignments file, uncollapsed, sorted (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - `BAM` index file (`.bam.bai`); from + - BAM index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) #### `intersect_extendend_primir` @@ -865,8 +1017,11 @@ Target rule as required by [Snakemake][docs-snakemake]. Intersect the aligned reads with the extended pri-miR annotations with [**BEDTools**](#third-party-software-used). +> Only those alignments fully intersecting a (possibly extended) pri-miR +> annotated region are kept. + - **Input** - - Alignments file (`.bam`); from + - Alignments file, sorted (`.bam`); from [**sort_all_alns_bam_by_position**](#sort_all_alns_bam_by_position) - pri-miR extended annotations (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) @@ -881,14 +1036,16 @@ Intersect the aligned reads with the extended pri-miR annotations with Remove alignments that do not intersect with any pri-miR with [**SAMtools**](#third-party-software-used). -> Required to only intersect alignments within a pri-miR locus. +> Required to only intersect alignments within a (possibly extended) pri-miR +> locus. - **Input** - - Alignments file (`.sam`); from [**filter_by_indels**](#filter_by_indels) + - Alignments file, filtered (`.sam`); from + [**filter_by_indels**](#filter_by_indels) - pri-miR intersections file (`.bed`); from [**intersect_extended_primir**](#intersect_extended_primir) - **Output** - - Alignments file, filtered (`.sam`); used in + - (Workflow output) Alignments file, filtered (`.sam`); used in [**convert_intersecting_primir_sam_to_bam**](#convert_intersecting_primir_sam_to_bam) and [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) @@ -899,10 +1056,10 @@ Convert alignments `.sam` file to `.bam` with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -with miRNA annotations. +> with miRNA annotations. - **Input** - - Alignments file (`.sam`); from + - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - **Output** - Alignments file (`.bam`); used in @@ -914,7 +1071,7 @@ with miRNA annotations. Sort alignments by position with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -with miRNA annotations more efficiently. +> with miRNA annotations more efficiently. - **Input** - Alignments file (`.bam`); from @@ -927,16 +1084,16 @@ with miRNA annotations more efficiently. #### `index_intersecting_primir_bam` -Create index `BAM` file with [**SAMtools**](#third-party-software-used). +Create index BAM file with [**SAMtools**](#third-party-software-used). > Indexing is required by genome viewers such as IGV to quickly display -alignments in a genomic region of interest. +> alignments in a genomic region of interest. - **Input** - - Alignments file (`.bam`); from + - Alignments file, sorted (`.bam`); from [**sort_intersecting_primir_bam_by_position**](#sort_intersecting_primir_bam_by_position) - **Output** - - `BAM` index file (`.bam.bai`); used in + - BAM index file (`.bam.bai`); used in [**intersect_extended_mirna**](#intersect_extended_mirna) @@ -945,13 +1102,16 @@ alignments in a genomic region of interest. Intersect the aligned reads with the extended miRNA annotations with [**BEDTools**](#third-party-software-used). +> Only those alignments fully intersecting an extended mature miRNA annotated +> region are kept. + - **Input** - - Alignments file (`.bam`); from + - Alignments file, sorted (`.bam`); from [**sort_intersecting_primir_bam_by_position**](#sort_intersecting_primir_bam_by_position) - - miRNA extended annotations (`.gff3`); from + - Mature miRNA extended annotations (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) - **Output** - - miRNA intersections file (`.bed`); used in + - Mature miRNA intersections file (`.bed`); used in [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) and [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) @@ -964,12 +1124,12 @@ Remove alignments that do not intersect with any miRNA with > Required to efficiently classify the alignments. - **Input** - - Alignments file (`.sam`); from + - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - - miRNA intersections file (`.bed`); from + - Mature miRNA intersections file (`.bed`); from [**intersect_extended_mirna**](#intersect_extended_mirna) - **Output** - - Alignments file, filtered (`.sam`); used in + - (Workflow output) Alignments file, filtered (`.sam`); used in [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) and [**uncollapse_reads**](#uncollapse_reads) @@ -979,29 +1139,73 @@ Remove alignments that do not intersect with any miRNA with Classify and add the intersecting (iso)miR to each alignment as a tag with a [**custom script**][custom-script-iso-tag]. -> To classify the reads, miRNA annotations are turned into the original ones. -The alignment start and end shifts relative to the annotations are computed -and append along with the `CIGAR` and `MD` strings to the intersecting miRNA. -If the read is classified as a canonical miRNA, the name will not include -the star and end shift, nor the `CIGAR` and `MD` strings. +> In this step, the mature miRNA annotated regions are used instead of the +> extended ones. Each alignment gets an extra tag (`YW:Z`) with either the +> (iso)miR(s) it is considered to really intersect with or an empty string +> otherwise. The format of the intersecting mature miRNA species is +> `miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and `3p-shift` are +> the difference between the miRNA start and end coordinates and the +> alignment's ones respectively. - **Input** - - Alignments file (`.sam`); from + - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - - miRNA intersections file (`.bed`); from + - Mature miRNA intersections file (`.bed`); from [**intersect_extended_mirna**](#intersect_extended_mirna) - **Parameters** - **config_template.yaml** - `extension`: Number of nucleotides by which mature miRNA annotated - regions are extended (default 6) + regions are extended (default: 6) - **Output** - Alignments file, tagged (`.sam`); used in [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) +- **Examples** + +```console +Example 1 | Intersecting a canoncial mature miRNA + +IN miRNA annotations: + chr19 . miRNA 44377 44398 . + . ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160 +IN SAM record: + 1-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 +NEW TAG: + YW:Z:hsa-miR-524-5p|0|0|22M|22 + + +Example 2 | Intersecting an isomiR (no shifts) + +IN miRNA annotations: + chr19 . miRNA 44377 44398 . + . ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160 +IN SAM record: + 1-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 +NEW TAG: + YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 + + +Example 3 | Intersecting an isomiR (no indels nor mismatches) + +IN miRNA annotations: + chr19 . miRNA 5338 5359 . + . ID=MIMAT0005795;Alias=MIMAT0005795;Name=hsa-miR-1323;Derives_from=MI0003786 +IN SAM record: + 1-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 +NEW TAG: + YW:Z:hsa-miR-1323|0|-1|21M|21 + + +Example 4 | Not intersecting an (iso)miR + +IN miRNA annotations: + chr19 . miRNA 5338 5359 . + . ID=MIMAT0005795;Alias=MIMAT0005795;Name=hsa-miR-1323;Derives_from=MI0003786 +IN SAM record: + 1-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 +NEW TAG: + YW:Z: +``` #### `sort_intersecting_mirna_by_feat_tag` -Sort the alignments by the tag containing the classified intersecting miRNA +Sort the alignments by the tag containing the classified intersecting (iso)miR with [**SAMtools**](#third-party-software-used). > Required for an efficient quantification. @@ -1016,65 +1220,85 @@ with [**SAMtools**](#third-party-software-used). #### `quantify_mirna` -Tabulate alignments according to its tag with a +Tabulate alignments according to its new tag (`YW:Z`) with a [**custom script**][custom-script-mir-quant]. -> Quantification is done with partial counts (_i.e._ each alignment contributes -by the number of collapsed reads divided by the number of hits). - -- **Input** - - Alignments file, sorted, tagged (`.sam`); from +> Each alignment contributes to the miRNA species in its `YW:Z` tag by `R/N`, +> where `R` is the number of collapsed reads in that alignment, and `N` is the +> number of genomic and/or transcriptomic loci it aligns to. The resulting +> table has a row for each mature miRNA species (isomiR, canonical miRNA or +> both) with the name format set in +> [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) unless +> considered a canonical miRNA, which only keeps the annotated mature miRNA +> name. A miRNA species is considered to be canonical if there are no shifts +> between its start and end positions and the aligned read ones, and there +> are no mismatches nor indels. + +- **Input** + - Alignments file, tagged, sorted (`.sam`); from [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - **Parameters** - **samples.tsv** - - Library name; specify in sample table column `sample` + - Library name; specified in the sample's table column `sample` - **config_template.yaml** - - `mir_list`: miRNA features to be quantified (default isomir, mirna + - `mir_list`: miRNA features to be quantified (default: isomir, mirna pri-miR) - **Output** - (iso)miR counts tab-delimited file; used in [**merge_tables**](#merge_tables) + #### `quantify_primir` Tabulate alignments according to its intersecting pri-miR with a [**custom script**][custom-script-pri-quant] -> Quantification is done with partial counts (_i.e._ each alignment contributes -by the number of collapsed reads divided by the number of hits). +> Each alignment contributes to the pri-miR it intersects with by `R/N`, where +> `R` is the number of collapsed reads in that alignment, and `N` is the +> number of genomic and/or transcriptomic loci it aligns to. The resulting +> table has a row for each pri-miR with the name format set in +> [**mirna_extension**](#mirna_extension). - **Input** - pri-miR intersections file (`.bed`); from - [**intersecti_extended_primir**](#intersect_extended_primir) + [**intersect_extended_primir**](#intersect_extended_primir) - **Output** - pri-miR counts tab-delimited file; used in [**merge_tables**](#merge_tables) + #### `merge_tables` Merge all the tables from the different libraries into a single one with a [**custom script**][custom-script-merge-tab]. +> The final table(s) containing the counting data from all libraries for the +> (iso)miRs and/or pri-miRs have a row per miRNA species and a column per +> sample library. If a miRNA species is not found in a certain library, its +> value is set to `NA`. + - **Input** - counts tab-delimited file; from [**quantify_mirna**](#quantify_mirna) and/or [**quantify_primir**](#quantify_primir) - **Parameters** - **cluster_schema.json** - - `mir_list`: miRNA features to be quantified (default isomir, mirna + - `mir_list`: miRNA features to be quantified (default: isomir, mirna pri-mir) - **Output** - - (iso)miR and/or pri-miR counts table (`.tab`) + - (Workflow output) (iso)miR and/or pri-miR counts table (`.tab`) + #### `uncollapse_reads` Reverse the collapsing of reads with identical sequences as done with -[**FASTX-Toolkit**](#third-party-software-used). +[**FASTX-Toolkit**](#third-party-software-used) with a +[**custom script**][custom-script-uncollapse]. - **Input** - - Alignments file (`.sam`); from + - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - **Output** - Uncollapsed aligned reads (`.sam`); used in @@ -1087,10 +1311,10 @@ Convert alignments `.sam` file to `.bam` with [**SAMtools**](#third-party-software-used). - **Input** - - Alignments file (`.sam`); from + - Alignments file, uncollapsed (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - **Output** - - Alignments file (`.bam`); used in + - Alignments file, uncollapsed (`.bam`); used in [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) @@ -1099,25 +1323,25 @@ Convert alignments `.sam` file to `.bam` with Sort alignments by position with [**SAMtools**](#third-party-software-used). - **Input** - - Alignments file (`.bam`); from + - Alignments file, uncollapsed (`.bam`); from [**convert_uncollapsed_reads_sam_to_bam**](#convert_uncollapsed_reads_sam_to_bam) - **Output** - - Alignments file, sorted (`.bam`); used in + - (Workflow output) Alignments file, uncollapsed, sorted (`.bam`); used in [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) #### `index_uncollapsed_reads_bam` -Create index `BAM` file with [**SAMtools**](#third-party-software-used). +Create index BAM file with [**SAMtools**](#third-party-software-used). > Indexing is required by genome viewers such as IGV to quickly display -alignments in a genomic region of interest. +> alignments in a genomic region of interest. - **Input** - - Alignments file (`.bam`); from + - (Workflow output) Alignments file, uncollapsed, sorted (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - **Output** - - `BAM` index file (`.bam.bai`) + - (Workflow output) BAM index file (`.bam.bai`) [chr-maps]: [custom-script-blocksort]: scripts/blocksort.sh @@ -1158,6 +1382,7 @@ alignments in a genomic region of interest. [license-gpl2]: [license-gpl3]: [license-mit]: +[oligomap-out]: [pub-bedtools]: [pub-cufflinks]: [pub-cutadapt]: From cde4393d8113ed71b16f840e82f8612455d9d7ef Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Fri, 5 Jan 2024 14:35:11 +0100 Subject: [PATCH 03/42] docs: fix typos --- pipeline_documentation.md | 67 ++++++++++++++++++++------------------- 1 file changed, 34 insertions(+), 33 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index b713244..1214733 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -79,8 +79,6 @@ on installation and usage please see [here](README.md). - [`sort_uncollapse_reads_bam_by_position`](#sort_uncollapse_reads_bam_by_position) - [`index_uncollapse_reads_bam`](#index_uncollapse_reads_bam) - - ## Third-party software used @@ -121,7 +119,7 @@ Visual representation of the workflow. Automatically prepared with ##### Requirements -- tab-separated values (`.tsv`) file +- Tab-separated values (`.tsv`) file - First row has to contain parameter names as in [`samples_table.tsv`](test/test_files/samples_table.tsv) - First column used as sample identifiers @@ -130,9 +128,8 @@ Parameter name | Description | Data type(s) --- | --- | --- sample | Arbitrary name for the miRNA sequence library. | `str` sample_file | Path to the `gzip`ped miRNA sequencing library file. The path must be relative to the directory where the workflow will be run. | `str` -adapter | Sequence of the 3'-end adapter used during library preparation. Required for [Cutadapt](#third-party-software-used). Use a value such as `XXXXXXXXXX` if no adapter is present or if no trimming is desired | `str` -format | One of `fa`/`fasta` or `fq`/`fastq`, if the library file is in FASTA or FASTQ format, respectively. - | `str` +adapter | Sequence of the 3'-end adapter used during library preparation. Required for [Cutadapt](#third-party-software-used). Use a value such as `XXXXXXXXXX` if no adapter is present or if no trimming is desired. | `str` +format | One of `fa`/`fasta` or `fq`/`fastq`, if the library file is in FASTA or FASTQ format, respectively. | `str` #### Configuration file @@ -141,6 +138,8 @@ Some parameters within the workflow can be modified. Refer to the [configuration template](#config/config_template.yaml) for a detailed explanation of each option. + + ### Snakefile #### `finish` @@ -150,15 +149,15 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - (Workflow output) SAM file with the pri-miR intersecting alignments; from - [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - - (Workflow output) SAM file with the mature miRNA intersecting alignments; from + - (**Workflow output**) SAM file with the pri-miR intersecting alignments; + from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) + - (**Workflow output**) SAM file with the mature miRNA intersecting alignments; from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - - (Workflow output) (iso)miR and/or pri-miR counts table (`.tab`); from + - (**Workflow output**) (iso)miR and/or pri-miR counts table (`.tab`); from [**merge_tables**](#merge_tables) - - (Workflow output) BAM file with the contributing alignments, sorted; from - [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - (Workflow output) BAM index file (`.bam.bai`); from + - (**Workflow output**) BAM file with the contributing alignments, sorted; + from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) + - (**Workflow output**) BAM index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) @@ -192,7 +191,7 @@ Target rule as required by [Snakemake][docs-snakemake]. Trim genome sequence IDs with a [**custom script**][custom-script-trim-id]. - **Input** - - (Workflow input) Genome sequence, `gzip`ed (`.fa.gz`/`.fasta.gz`) + - (**Workflow input**) Genome sequence, `gzip`ed (`.fa.gz`/`.fasta.gz`) - **Output** - Genome sequence, trimmed IDs (`.fa`); used in [**extract_transcriptome_seqs**](#extract_transcriptome_seqs), @@ -205,13 +204,13 @@ Trim genome sequence IDs with a [**custom script**][custom-script-trim-id]. #### `extract_transcriptome_seqs` -Create transcriptome from genome sequence and annotations with +Create transcriptome from genomic sequence and annotations with [**cufflinks**](#third-party-software-used). - **Input** - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - - (Workflow input) Genome annotations, `gzip`ed (`.gtf.gz`) + - (**Workflow input**) Genome annotations, `gzip`ed (`.gtf.gz`) - **Output** - Transcriptome sequence (`.fa`); used in [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) @@ -238,14 +237,14 @@ Generate transcriptome index for [**segemehl**](#third-party-software-used) short read aligner. > The transcriptome index only needs to be generated once for each combination -> of genome and annotations and sample sets. +> of transcriptome sequence and annotations, and sample sets. - **Input** - Transcriptome sequence, trimmed IDs (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - **Output** - segemehl transcriptome index (`.idx`); used in - [**mapping_genome_segemehl**](#mapping_genome_segemehl) + [**mapping_transcriptome_segemehl**](#mapping_transcriptome_segemehl) #### `generate_segemehl_index_genome` @@ -270,7 +269,7 @@ Retrieve exon annotations from genome annotations with a [**custom script**][custom-script-get-lines]. - **Input** - - (Workflow input) Genome annotations, `gzip`ed (`.gtf.gz`) + - (**Workflow input**) Genome annotations, `gzip`ed (`.gtf.gz`) - **Output** - Exon annotations (`.gtf`); used in [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) @@ -312,8 +311,8 @@ with a [**custom script**][custom-script-map-chr]. > miRNA annotations. Several mapping tables are available [here][chr-maps]. - **Input** - - (Workflow input) miRNA annotations (`.gff3`) - - (Workflow input) Tab-separated chromosome name mappings table (`.tsv`) + - (**Workflow input**) miRNA annotations (`.gff3`) + - (**Workflow input**) Tab-separated chromosome name mappings table (`.tsv`) - **Output** - miRNA annotations, mapped chromosome name(s) (`.gff3`); used in [**extend_mirs_annotations**](#extend_mirs_annotations) @@ -336,6 +335,8 @@ Create a FASTA index for the genome with Extract chromosome(s) length from the genome sequence. + + - **Input** - FASTA genome index (`.fa.fai`); from [**create_index_genome_fasta**](#create_index_genome_fasta) @@ -438,10 +439,10 @@ Copy and rename read files. > Local rule. > Depending on the library file format, the output file undergoes a quality -> filter (`.fastq`) or is directly formatted (`.fa`). +> filter (`fa`/`.fastq`) or is directly formatted (`.fa`/`.fasta`). - **Input** - - (Workflow input) miRNA sequencing library, `gzip`ed + - (**Workflow input**) miRNA sequencing library, `gzip`ed (`.fa.gz`/`.fasta.gz` or `.fq.gz`/`.fastq.gz`) - **Output** - miRNA sequencing library, copied, renamed (`.fa`, `.fastq`); used in @@ -495,8 +496,8 @@ Format read's sequences to appear on a single line with #### `remove_adapters` -Trim adapters and `N` bases at either end. Filter reads by minimum length and -number of inner `N` bases with [**cutadapt**](#third-party-software-used). +Trim 3' adapters and `N` bases at either end. Filter reads by minimum length +and number of inner `N` bases with [**cutadapt**](#third-party-software-used). - **Input** - miRNA sequencing library, formatted (`.fa`); from @@ -511,8 +512,8 @@ number of inner `N` bases with [**cutadapt**](#third-party-software-used). bases (default: 3) - `minimum_length`: Minimum length for a processed read to be kept (default: 15) - - `max_n`: Maximum number of `N` bases for a processed read to be kept - (default: 0) + - `max_n`: Maximum number of inner `N` bases for a processed read to be + kept (default: 0) - **Output** - miRNA sequencing library, filtered, without adapters (`.fasta`); used in [**collapse_identical_reads**](#collapse_identical_reads) @@ -1045,7 +1046,7 @@ Remove alignments that do not intersect with any pri-miR with - pri-miR intersections file (`.bed`); from [**intersect_extended_primir**](#intersect_extended_primir) - **Output** - - (Workflow output) Alignments file, filtered (`.sam`); used in + - (**Workflow output**) Alignments file, filtered (`.sam`); used in [**convert_intersecting_primir_sam_to_bam**](#convert_intersecting_primir_sam_to_bam) and [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) @@ -1129,7 +1130,7 @@ Remove alignments that do not intersect with any miRNA with - Mature miRNA intersections file (`.bed`); from [**intersect_extended_mirna**](#intersect_extended_mirna) - **Output** - - (Workflow output) Alignments file, filtered (`.sam`); used in + - (**Workflow output**) Alignments file, filtered (`.sam`); used in [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) and [**uncollapse_reads**](#uncollapse_reads) @@ -1287,7 +1288,7 @@ Merge all the tables from the different libraries into a single one with a - `mir_list`: miRNA features to be quantified (default: isomir, mirna pri-mir) - **Output** - - (Workflow output) (iso)miR and/or pri-miR counts table (`.tab`) + - (**Workflow output**) (iso)miR and/or pri-miR counts table (`.tab`) @@ -1326,7 +1327,7 @@ Sort alignments by position with [**SAMtools**](#third-party-software-used). - Alignments file, uncollapsed (`.bam`); from [**convert_uncollapsed_reads_sam_to_bam**](#convert_uncollapsed_reads_sam_to_bam) - **Output** - - (Workflow output) Alignments file, uncollapsed, sorted (`.bam`); used in + - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); used in [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) @@ -1338,10 +1339,10 @@ Create index BAM file with [**SAMtools**](#third-party-software-used). > alignments in a genomic region of interest. - **Input** - - (Workflow output) Alignments file, uncollapsed, sorted (`.bam`); from + - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - **Output** - - (Workflow output) BAM index file (`.bam.bai`) + - (**Workflow output**) BAM index file (`.bam.bai`) [chr-maps]: [custom-script-blocksort]: scripts/blocksort.sh From ce4e5b7326e6670dafb8ac89f9b096c8866a73f0 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Mon, 29 Jan 2024 17:39:05 +0100 Subject: [PATCH 04/42] docs: update rules --- pipeline_documentation.md | 80 +++++++++++++++++++-------------------- 1 file changed, 38 insertions(+), 42 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index 493eed2..ede83d5 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -167,7 +167,7 @@ Target rule as required by [Snakemake][docs-snakemake]. from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - (**Workflow output**) BAM index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - - Empty text file (`.txt`); from + - (**Workflow output**) Empty text file (`.txt`) [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -445,7 +445,7 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - BAM index (`.bam.bai`); from + - BAM index file (`.bam.bai`); from [**index_all_alns_bam**](#index_all_alns_bam) #### `start` @@ -622,7 +622,7 @@ Align short reads to reference genome with - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - Alignments file (`.fasta`); used in + - Alignments file (`.oligomap`); used in [**sort_genome_oligomap**](#sort_genome_oligomap) - Alignment report (`.txt`); used in [**sort_genome_oligomap**](#sort_genome_oligomap) @@ -634,18 +634,16 @@ Sort [**oligomap**](#third-party-software-used) alignments by query name with a [**custom script**][custom-script-blocksort]. - **Input** - - Alignments file (`.fasta`); from - [**map_genome_oligomap**](#map_genome_oligomap) - - Alignment report (`.txt`); from + - Alignments file (`.oligomap`); from [**map_genome_oligomap**](#map_genome_oligomap) - **Output** - - Alignments file, sorted (`.fasta`); used in + - Alignments file, sorted (`.oligomap`); used in [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) #### `convert_genome_to_sam_oligomap` -Convert aligned reads `.fasta` to `.sam` and filter alignments by number of +Convert aligned reads `.oligomap` to `.sam` and filter alignments by number of hits with a [**custom script**][custom-script-oligo-sam]. > Given the short length of the reads and the sequence similarity among miRNAs, @@ -653,7 +651,7 @@ hits with a [**custom script**][custom-script-oligo-sam]. > specified value are disregarded. - **Input** - - Alignments file, sorted (`.fasta`); from + - Alignments file, sorted (`.oligomap`); from [**sort_genome_oligomap**](#sort_genome_oligomap) - **Parameters** - **config_template.yaml** @@ -677,7 +675,7 @@ Align short reads to reference transcriptome with - Transcriptome sequence, trimmed IDs (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - **Output** - - Alignments file (`.fasta`); used in + - Alignments file (`.oligomap`); used in [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - Alignment report (`.txt`); used in [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) @@ -689,18 +687,16 @@ Sort [**oligomap**](#third-party-software-used) alignments by query name with a [**custom script**][custom-script-blocksort]. - **Input** - - Alignments file (`.fasta`); from - [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) - - Alignment report (`.txt`); from + - Alignments file (`.oligomap`); from [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) - **Output** - - Alignments file, sorted (`.fasta`); used in + - Alignments file, sorted (`.oligomap`); used in [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptome_to_sam_oligomap) #### `convert_transcriptome_to_sam_oligomap` -Convert aligned reads `.fasta` to `.sam` and filter alignments by number of +Convert aligned reads `.oligomap` to `.sam` and filter alignments by number of hits with a [**custom script**][custom-script-oligo-sam]. > Given the short length of the reads and the sequence similarity among miRNAs, @@ -708,7 +704,7 @@ hits with a [**custom script**][custom-script-oligo-sam]. > specified value are disregarded. - **Input** - - Alignments file, sorted (`.fasta`); from + - Alignments file, sorted (`.oligomap`); from [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - **Parameters** - **config_template.yaml** @@ -1019,8 +1015,7 @@ Target rule as required by [Snakemake][docs-snakemake]. - **Input** - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - - Alignments file, filtered (`.sam`); from - [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) + and [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - (iso)miR and/or pri-miR counts table (`.tab`); from [**merge_tables**](#merge_tables) - Alignments file, uncollapsed, sorted (`.bam`); from @@ -1028,6 +1023,7 @@ Target rule as required by [Snakemake][docs-snakemake]. - BAM index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) + #### `intersect_extendend_primir` Intersect the aligned reads with the extended pri-miR annotations with @@ -1254,7 +1250,7 @@ Tabulate alignments according to its new tag (`YW:Z`) with a [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - **Parameters** - **samples.tsv** - - Library name; specified in the sample's table column `sample` + - Library name; specified in the samples table column `sample` - **config_template.yaml** - `mir_list`: miRNA features to be quantified (default: isomir, mirna pri-miR) @@ -1295,7 +1291,7 @@ Merge all the tables from the different libraries into a single one with a > value is set to `NA`. - **Input** - - counts tab-delimited file; from [**quantify_mirna**](#quantify_mirna) + - Counts tab-delimited file; from [**quantify_mirna**](#quantify_mirna) and/or [**quantify_primir**](#quantify_primir) - **Parameters** - **cluster_schema.json** @@ -1373,7 +1369,7 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - Empty text files (`.txt`); from + - (**Workflow output**) Empty text file (`.txt`) [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups) and [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) @@ -1391,7 +1387,7 @@ Create an empty BED file if the user has not provided one. - `bed_file`: BED6 file with all the desired annotation regions to perform the ASCII-style alignment pileups on. (Default: None) - **Output** - - BED empty file (`.bed`); used in + - Empty BED file (`.bed`); used in [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -1406,10 +1402,10 @@ Compress the processed genome with trimmed IDs using `bgzip`. > using Singularity, [**SAMtools**](#third-party-software-used) is used. - **Input** - - Genome sequence file, trimmed IDs (`.fa`); from + - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); used in + - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); used in [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -1418,25 +1414,25 @@ Compress the processed genome with trimmed IDs using `bgzip`. #### `create_per_library_ascii_pileups` Create ASCII-style pileups for all the desired annotated regions across -libraries with [**ASCII-style alignment pilueups**](#third-party-software-used). +libraries with [**ASCII-style alignment pileups**](#third-party-software-used). > A directory containing the ASCII-style pileups is created for each > library. If no BED file is provided, the pileups' output directories will > only contain an empty file. - **Input** - - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); from + - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); from [**compress_reference_genome**](#compress_reference_genome) - - miRNA annotations with mapped genes(`.gff3`); from + - miRNA annotations, mapped chromosome name(s) (`.gff3`); from [**map_chr_names**](#map_chr_names) - - Alignments file (`.bam`); from + - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - `BAM` index file (`.bam.bai`); from + - (**Workflow output**) BAM index file (`.bam.bai`); used in [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - Annotated genomic regions (`.bed`); from workflow input files or [**create_empty_bed**](#create_empty_bed) - **Output** - - Empty text file (`.txt`) + - (**Workflow output**) Empty text file (`.txt`) #### `create_per_run_ascii_pileups` @@ -1448,18 +1444,18 @@ run with [**ASCII-style alignment pilueups**](#third-party-software-used). > an empty file. - **Input** - - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); from + - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); from [**compress_reference_genome**](#compress_reference_genome) - - miRNA annotations with mapped genes(`.gff3`); from + - miRNA annotations, mapped chromosome name(s) (`.gff3`); from [**map_chr_names**](#map_chr_names) - - Alignments file (`.bam`); from + - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - `BAM` index file (`.bam.bai`); from + - (**Workflow output**) BAM index file (`.bam.bai`); used in [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - Annotated genomic regions (`.bed`); from workflow input files or [**create_empty_bed**](#create_empty_bed) - **Output** - - Empty text file (`.txt`) + - (**Workflow output**) Empty text file (`.txt`) #### `create_per_condition_ascii_pileups` @@ -1474,21 +1470,21 @@ different library subsets if provided with > executed, and no output will be generated. - **Input** - - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); from + - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); from [**compress_reference_genome**](#compress_reference_genome) - - miRNA annotations with mapped genes(`.gff3`); from + - miRNA annotations, mapped chromosome name(s) (`.gff3`); from [**map_chr_names**](#map_chr_names) - - Alignments file (`.bam`); from + - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - `BAM` index file (`.bam.bai`); from + - (**Workflow output**) BAM index file (`.bam.bai`); used in [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - Annotated genomic regions (`.bed`); from workflow input files or [**create_empty_bed**](#create_empty_bed) - **Parameters** - **config_template.yaml** - - `lib_dict`: Subset(s) of library name(s), as specified in the samples' - table column `sample` and the subset identifier stored in a dictionary. - (default: None) + - `lib_dict`: Dictionary of arbitrary condition names (keys) and library + names to aggregate alignment pileups for (values; MUST correspond to names + in samples table) (default: None) - **Output** - Empty text file (`.txt`) From 4dfe8be81ea9bbc677f415a88a9488ec0161f2f3 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Tue, 30 Jan 2024 12:48:17 +0100 Subject: [PATCH 05/42] docs: update rules --- pipeline_documentation.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index ede83d5..c1a26ff 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -384,7 +384,6 @@ Extend miRNA annotations and split the file by feature with a [**intersect_extended_primir**](#intersect_extended_primir) - Mature miRNA (miRNA) extended annotations (`.gff3`); used in [**intersect_extended_mirna**](#intersect_extended_mirna) - - **Examples** ```console @@ -764,6 +763,7 @@ Filter merged genome alignments by the number of hits with a - Alignments file, filtered (`.sam`); used in [**remove_header_genome_mappings**](#remove_header_genome_mappings) + #### `filter_transcriptome_by_nh` Filter merged transcriptome alignments by the number of hits with a @@ -874,7 +874,6 @@ Remove duplicate and inferior alignments with a > a bigger edit distance than the smaller one within the group. The tags `NH` > (number of hits) and `HI` (query hit index) are updated accordingly. - - **Input** - Alignments file, sorted (`.sam`); from [**sort_maps_by_id**](#sort_maps_by_id) @@ -916,6 +915,7 @@ OUT: 1-1197 256 19 76967 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:1 NH:i:2 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 ``` + #### `filter_by_indels` Filter multimappers favoring mismatches over indels with a @@ -1257,8 +1257,12 @@ Tabulate alignments according to its new tag (`YW:Z`) with a - **Output** - (iso)miR counts tab-delimited file; used in [**merge_tables**](#merge_tables) +- **Examples** + +```console + +``` - #### `quantify_primir` @@ -1488,6 +1492,7 @@ different library subsets if provided with - **Output** - Empty text file (`.txt`) + [chr-maps]: [custom-script-blocksort]: scripts/blocksort.sh [custom-script-filter-mm]: scripts/filter_multimappers.py From 9f8f99eea263a3ad63ac89a90cc9e72be0f3a3c7 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Tue, 30 Jan 2024 13:39:26 +0100 Subject: [PATCH 06/42] fix: set correct wildcard --- workflow/rules/pileup.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/pileup.smk b/workflow/rules/pileup.smk index 97654c3..00768c2 100644 --- a/workflow/rules/pileup.smk +++ b/workflow/rules/pileup.smk @@ -139,7 +139,7 @@ rule create_per_library_ascii_pileups: params: cluster_log=CLUSTER_LOG / "pileups_{sample}.log", out_dir=lambda wildcards: expand( - PILEUP_DIR / "{sample}", sample=pd.unique(samples_table.index.values) + PILEUP_DIR / "{sample}", sample=[wildcards.sample] ), prefix="{sample}", log: From 1e345dd5900dc1fedff58793c824603aa174a609 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Wed, 31 Jan 2024 14:03:32 +0100 Subject: [PATCH 07/42] docs: complete rules improvement --- pipeline_documentation.md | 200 ++++++++++++++++++++++++++++++++------ 1 file changed, 172 insertions(+), 28 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index c1a26ff..5f2a807 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -105,7 +105,7 @@ on installation and usage please see [here](README.md). ## Description of workflow steps -> The workflow consists of four Snakemake files: A main `Snakefile` and an +> The workflow consists of five Snakemake files: A main `Snakefile` and an > individual Snakemake file for each step in the workflow (the genome resources > preparation, the reads mapping, the miRNA quantification and the ASCII-style > pileups generation). The main `Snakefile` contains the configuration file @@ -146,7 +146,6 @@ Some parameters within the workflow can be modified. Refer to the [configuration template](#config/config_template.yaml) for a detailed explanation of each option. - ### Snakefile @@ -221,9 +220,9 @@ Create transcriptome from genomic sequence and annotations with [**cufflinks**](#third-party-software-used). - **Input** + - (**Workflow input**) Genome annotations, `gzip`ed (`.gtf.gz`) - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - - (**Workflow input**) Genome annotations, `gzip`ed (`.gtf.gz`) - **Output** - Transcriptome sequence (`.fa`); used in [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) @@ -287,6 +286,7 @@ Retrieve exon annotations from genome annotations with a - Exon annotations (`.gtf`); used in [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) + #### `convert_exons_gtf_to_bed` Convert exon annotations `.gtf` to `.bed` with a @@ -305,7 +305,7 @@ Create SAM header for the genome with [**SAMtools**](#third-party-software-used). > Required by [SAMtools](#third-party-software-used) to work with the -> alignments file. +> alignment files. - **Input** - Genome sequence, trimmed IDs (`.fa`); from @@ -350,7 +350,9 @@ Create a FASTA index for the genome with Extract chromosome(s) length from the genome sequence. - +> Required to ensure that the extended annotations in generated in the +> [**extend_mirs_annotations**](#extend_mirs_annotations) rule do not exceed +> the chromosome(s) boundaries. - **Input** - FASTA genome index (`.fa.fai`); from @@ -369,8 +371,8 @@ Extend miRNA annotations and split the file by feature with a > with shifted start and/or end positions without exceeding chromosome(s) > boundaries. If required, pri-miR loci are also extended to accommodate the > new miRNA coordinates. In addition, pri-miR names are modified to record the -> final positions by appending `_-y` and `_+x` to it, where `y` is the 5' -> shift and `x` the 3' shift. +> final positions by appending `_-y` and `_+x` to them, where `y` is the 5' +> shift and `x` the 3' shift. - **Input** - miRNA annotations, mapped chromosome name(s) (`.gff3`); from @@ -447,6 +449,7 @@ Target rule as required by [Snakemake][docs-snakemake]. - BAM index file (`.bam.bai`); from [**index_all_alns_bam**](#index_all_alns_bam) + #### `start` Copy and rename read files. @@ -495,6 +498,7 @@ Convert reads file from FASTQ to FASTA with - **Output** - miRNA sequencing library (`.fa`); used in [**format_fasta**](#format_fasta) + #### `format_fasta` Format read's sequences to appear on a single line with @@ -504,7 +508,7 @@ Format read's sequences to appear on a single line with - miRNA sequencing library (`.fa`); from [**start**](#start) or [**fastq_to_fasta**](#fastq_to_fasta) - **Output** - - miRNA sequencing library, formatted (`.fa`); used in + - miRNA sequencing library, formatted (`.fasta`); used in [**remove_adapters**](#remove_adapters) @@ -514,7 +518,7 @@ Trim 3' adapters and `N` bases at either end. Filter reads by minimum length and number of inner `N` bases with [**cutadapt**](#third-party-software-used). - **Input** - - miRNA sequencing library, formatted (`.fa`); from + - miRNA sequencing library, formatted (`.fasta`); from [**format_fasta**](#format_fasta) - **Parameters** - **samples.tsv** @@ -562,7 +566,7 @@ Align short reads to reference genome with [**collapse_identical_reads**](#collapse_identical_reads) - Genome sequence, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - - segemehl genome index (`idx`); from + - segemehl genome index (`.idx`); from [**generate_segemehl_index_genome**](#generate_segemehl_index_genome) - **Output** - Alignments file (`.sam`); used in @@ -575,11 +579,11 @@ Align short reads to reference transcriptome with [**segemehl**](#third-party-software-used). - **Input** - - miRNA sequencing library, collapsed (`.fa`); from + - miRNA sequencing library, collapsed, renamed (`.fasta`); from [**collapse_identical_reads**](#collapse_identical_reads) - Transcriptome sequence, trimmed IDs (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - - segemehl transcriptome index (`idx`); from + - segemehl transcriptome index (`.idx`); from [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome) - **Output** - Alignments file (`.sam`); used in @@ -590,7 +594,7 @@ Align short reads to reference transcriptome with Filter reads by length with a [**custom script**][custom-script-validation]. -> Required for the mapping optimal speed. Oligomap is specifically written for +> Required for an optimal mapping speed. Oligomap is specifically written for > short reads. Therefore, reads with more bases than the default maximum (30 > nts) makes the mapping slower. @@ -623,8 +627,7 @@ Align short reads to reference genome with - **Output** - Alignments file (`.oligomap`); used in [**sort_genome_oligomap**](#sort_genome_oligomap) - - Alignment report (`.txt`); used in - [**sort_genome_oligomap**](#sort_genome_oligomap) + - Alignments report (`.txt`) #### `sort_genome_oligomap` @@ -676,8 +679,7 @@ Align short reads to reference transcriptome with - **Output** - Alignments file (`.oligomap`); used in [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - - Alignment report (`.txt`); used in - [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) + - Alignments report (`.txt`) #### `sort_transcriptome_oligomap` @@ -813,7 +815,7 @@ Remove the SAM header of the transcriptome alignments file with #### `transcriptome_to_genome_maps` -Convert the alignment's transcriptome coordinates to genomic ones with a +Convert the alignments' transcriptome coordinates to genomic ones with a [**custom script**][custom-script-sam-trx]. - **Input** @@ -828,7 +830,7 @@ Convert the alignment's transcriptome coordinates to genomic ones with a #### `merge_all_maps` -Concatenate the four alignments files into a single file. +Concatenate the four alignment files into a single one. - **Input** - Alignments files, without SAM header (`.sam`); from @@ -958,6 +960,7 @@ OUT: 1-1 16 19 545543 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14A0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:1 ``` + #### `convert_all_alns_sam_to_bam` Convert alignments `.sam` file to `.bam` with @@ -1236,9 +1239,10 @@ Tabulate alignments according to its new tag (`YW:Z`) with a > Each alignment contributes to the miRNA species in its `YW:Z` tag by `R/N`, > where `R` is the number of collapsed reads in that alignment, and `N` is the -> number of genomic and/or transcriptomic loci it aligns to. The resulting -> table has a row for each mature miRNA species (isomiR, canonical miRNA or -> both) with the name format set in +> number of genomic and/or transcriptomic loci it aligns to. The values of +> both, `R` and `N` are inferred from the sequence name which follows the +> format `ID-R_N`. The resulting table has a row for each mature miRNA species +> (isomiR, canonical miRNA or both) with the name format set in > [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) unless > considered a canonical miRNA, which only keeps the annotated mature miRNA > name. A miRNA species is considered to be canonical if there are no shifts @@ -1250,7 +1254,7 @@ Tabulate alignments according to its new tag (`YW:Z`) with a [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - **Parameters** - **samples.tsv** - - Library name; specified in the samples table column `sample` + - Library name; specified in the sample's table column `sample` - **config_template.yaml** - `mir_list`: miRNA features to be quantified (default: isomir, mirna pri-miR) @@ -1260,7 +1264,71 @@ Tabulate alignments according to its new tag (`YW:Z`) with a - **Examples** ```console +Example 1 | Canonical miRNA and isomiR + +IN SAM record: + 10-4_2 0 19 34627 255 21M * 0 0 AAAGTGCTTCCTTTTAGAGGG * MD:Z:21 NM:i:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-520b-3p|0|0|21M|21 + 10-4_2 0 19 40866 255 21M * 0 0 AAAGTGCTTCCTTTTAGAGGG * MD:Z:21 NM:i:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-520c-3p|0|-1|21M|21 + +Data: + Alignment: + Read ID: 10 + Number of collapsed reads: 4 + Number of mapped genomic loci: 2 + Contribution: 4/2 = 2 + miRNA species: + Tag name: hsa-miR-520b-3p|0|0|21M|21 + Type: Canonical + Table name: hsa-miR-520b-3p + Total count: 2 + + Tag name: hsa-miR-520c-3p|0|-1|21M|21 + Type: isomiR + Table name: hsa-miR-520c-3p|0|-1|21M|21 + Total count: 2 + +OUT table: + ID lib_name + hsa-miR-520b-3p 2 + hsa-miR-520c-3p|0|-1|21M|21 2 + + +Example 2 | Different isomiRs + +IN SAM record: + 599-1_3 0 19 27804 255 20M * 0 0 AAAGTGCTTCCTTTTAGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-526b-3p|1|-1|20M|20 + 599-1_3 0 19 34627 255 20M * 0 0 AAAGTGCTTCCTTTTAGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520b-3p|0|-1|20M|20 + 599-1_3 0 19 40866 255 20M * 0 0 AAAGTGCTTCCTTTTAGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520c-3p|0|-2|20M|20 + +Data: + Alignment: + Read ID: 599 + Number of collapsed reads: 1 + Number of mapped genomic loci: 3 + Contribution: 1/3 = 0.33 + + miRNA species: + Tag name: hsa-miR-526b-3p|1|-1|20M|20 + Type: isomiR + Table name: hsa-miR-526b-3p|1|-1|20M|20 + Total count: 0.33 + + Tag name: hsa-miR-520b-3p|0|-1|20M|20 + Type: isomiR + Table name: hsa-miR-520b-3p|0|-1|20M|20 + Total count: 0.33 + + Tag name: hsa-miR-520c-3p|0|-2|20M|20 + Type: isomiR + Table name: hsa-miR-520c-3p|0|-2|20M|20 + Total count: 0.33 + +OUT table: + ID lib_name + hsa-miR-520b-3p|0|-1|20M|20 0.33 + hsa-miR-520c-3p|0|-2|20M|20 0.33 + hsa-miR-526b-3p|1|-1|20M|20 0.33 ``` @@ -1271,9 +1339,10 @@ Tabulate alignments according to its intersecting pri-miR with a > Each alignment contributes to the pri-miR it intersects with by `R/N`, where > `R` is the number of collapsed reads in that alignment, and `N` is the -> number of genomic and/or transcriptomic loci it aligns to. The resulting -> table has a row for each pri-miR with the name format set in -> [**mirna_extension**](#mirna_extension). +> number of genomic and/or transcriptomic loci it aligns to. The values of +> both, `R` and `N` are inferred from the sequence name which follows the +> format `ID-R_N`. The resulting table has a row for each pri-miR with the +> name format set in [**mirna_extension**](#mirna_extension). - **Input** - pri-miR intersections file (`.bed`); from @@ -1281,8 +1350,61 @@ Tabulate alignments according to its intersecting pri-miR with a - **Output** - pri-miR counts tab-delimited file; used in [**merge_tables**](#merge_tables) +- **Examples** + +```console +Example 1 | One single pri-miR with different alignments + +IN BED records: + 19 . miRNA_primary_transcript 27766 27788 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27765 27788 68-2_1 255 + + 19 . miRNA_primary_transcript 27766 27787 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27765 27787 316-1_7 1 + + 19 . miRNA_primary_transcript 27804 27823 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27803 27823 599-1_3 255 + + 19 . miRNA_primary_transcript 27805 27822 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27804 27822 226-1_4 1 + + +Alignments: + Read ID: 68 + Number of collapsed reads: 2 + Number of mapped genomic loci: 1 + Contribution: 2/1 = 2 + + Read ID: 316 + Number of collapsed reads: 1 + Number of mapped genomic loci: 7 + Contribution: 1/7 = 0.143 + + Read ID: 599 + Number of collapsed reads: 1 + Number of mapped genomic loci: 3 + Contribution: 1/3 = 0.33 + + Read ID: 226 + Number of collapsed reads: 1 + Number of mapped genomic loci: 4 + Contribution: 1/4 = 0.25 + +OUT table: + ID lib_name + hsa-mir-526b_-0_+0 2.723 + + +Example 2 | Different pri-miRs for a single read + +IN BED records: + 19 . miRNA_primary_transcript 40866 40886 . + . ID=MI0003158;Alias=MI0003158;Name=hsa-mir-520c_-0_+0 19 40865 40886 10-4_2 255 + + 19 . miRNA_primary_transcript 34627 34647 . + . ID=MI0003155;Alias=MI0003155;Name=hsa-mir-520b_-5_+6 19 34626 34647 10-4_2 255 + + +Alignment: + Read ID: 10 + Number of collapsed reads: 4 + Number of mapped genomic loci: 2 + Contribution: 4/2 = 2 + +OUT table: + ID lib_name + hsa-mir-520c_-0_+0 2 + hsa-mir-520b_-5_+6 2 +``` - #### `merge_tables` @@ -1303,8 +1425,30 @@ Merge all the tables from the different libraries into a single one with a pri-mir) - **Output** - (**Workflow output**) (iso)miR and/or pri-miR counts table (`.tab`) +- **Example** + +```console +IN library 1 + ID lib_1 + hsa-miR-524-5p 1 + hsa-miR-524-5p|0|0|22M|9G12 1 + hsa-miR-524-5p|0|0|22M|9G9C2 1 + +IN library 2 + ID lib_2 + hsa-miR-524-5p 1 + hsa-miR-1283 1 + hsa-miR-1283|-1|-2|21M|21 1 + +OUT table + ID lib_1 lib_2 + hsa-miR-524-5p 1 1 + hsa-miR-524-5p|0|0|22M|9G12 1 NA + hsa-miR-524-5p|0|0|22M|9G9C2 1 NA + hsa-miR-1283 NA 1 + hsa-miR-1283|-1|-2|21M|21 NA 1 +``` - #### `uncollapse_reads` From a4049b151f650dfe0b2cac98f62baa92933f3aa0 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Fri, 23 Feb 2024 18:17:27 +0100 Subject: [PATCH 08/42] revert: undo refactoring --- workflow/rules/pileup.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/pileup.smk b/workflow/rules/pileup.smk index 00768c2..97654c3 100644 --- a/workflow/rules/pileup.smk +++ b/workflow/rules/pileup.smk @@ -139,7 +139,7 @@ rule create_per_library_ascii_pileups: params: cluster_log=CLUSTER_LOG / "pileups_{sample}.log", out_dir=lambda wildcards: expand( - PILEUP_DIR / "{sample}", sample=[wildcards.sample] + PILEUP_DIR / "{sample}", sample=pd.unique(samples_table.index.values) ), prefix="{sample}", log: From 1eeb07a59d2dbfac275c7445f79c04753424f9b9 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Tue, 7 May 2024 15:12:24 +0200 Subject: [PATCH 09/42] docs: update main README --- README.md | 79 ++++++++++++++++++++++++++++++++----------------------- 1 file changed, 46 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index e86865a..2fec1ef 100644 --- a/README.md +++ b/README.md @@ -159,7 +159,7 @@ tested, you can go ahead and run the workflow on your samples. It is suggested to have all the input files for a given run (or hard links pointing to them) inside a dedicated directory, for instance under the _MIRFLOWZ_ root directory. This way, it is easier to keep the data together, -reproduce analysis and set up Singularity access to them. +set up Singularity access to them and reproduce analyses. #### 1. Prepare a sample table @@ -325,41 +325,54 @@ snakemake \ The _MIRFLOWZ_ workflow initially processes and indexes the genome resources provided by the user. The regions corresponding to mature miRNAs are extended -on both sides to accommodate isomiR species with shifted start and/or end -positions. If necessary, pri-miR loci are similarly extended to adjust to the -new miRNA coordinates. - -Subsequently, the user-provided short-read small RNA-seq libraries undergo -quality filtering if a FASTQ file is provided. Alternatively, adapters are -directly removed. The resulting reads are independently mapped to both the -genome and the transcriptome using two distinct aligners: [Segemehl][segemehl] -and our in-house tool [Oligomap][oligomap]. After the mapping, only the best -alignments for each read, determined by the smallest edit distance, are -retained by merging and filtering the resulting alignments into a single file. - -The collection of resulting alignments is then reduced to contain only unique -entries. Due to the short length of the reads and the sequence similarity among +by a fixed but user-adjustable number of nucleotides on both sides to +accommodate isomiR species with shifted start and/or end positions. If +necessary, pri-miR loci are extended to adjust to the new miRNA coordinates. +The user-provided short-read small RNA-seq libraries undergo quality filtering +(skipped if libraries are provided in FASTA rather than FASTQ), followed by +adapter removal. + +The resulting reads are independently mapped to both the genome and the +transcriptome using two distinct aligners: Segemehl and our in-house tool +Oligomap. On the one hand, Segemehl implements a fast heuristic strategy that +returns the alignment(s) with the smallest edit distance. Oligomap, on the +other hand, implements a slower and more restricted approach that reports all +the alignments with an edit distance of at most 1. The combination of the fast +and flexible results and the strict selection ensures results with a higher +fidelity than if only one of the tools were to be used. After the mapping, +duplicate alignments resulting from the partially redundant mapping strategy +are discarded and only the best alignments for each read are retained in a +a single file. + + + +Finally, to visualize the distribution of read alignments around miRNA +loci, ASCII-style alignment pileups are optionally generated for user-defined +regions of interest. > **NOTE:** For a detailed description of each rule along with some examples, > please, refer to the [workflow documentation](pipeline_documentation.md). @@ -375,7 +388,7 @@ _MIRFLOWZ_ is an open-source project which relies on community contributions. You are welcome to participate by submitting bug reports or feature requests, taking part in discussions, or proposing fixes and other code changes. Please refer to the [contributing guidelines](CONTRIBUTING.md) if you are interested -in contribute. +in contributing. ## License @@ -384,7 +397,7 @@ This project is covered by the [MIT License](LICENSE). ## Contact For questions or suggestions regarding the code, please use the -[issue tracker][issue-tracker]. Do not hesitate on contacting us via +[issue tracker][issue-tracker]. Do not hesitate to contact us via [email][email] for any other inquiries. © 2023 [Zavolab, Biozentrum, University of Basel][zavolab] From ada71c030fdc09dcc7616524fec2362da70e055c Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Tue, 7 May 2024 15:12:44 +0200 Subject: [PATCH 10/42] docs: update pipeline documentation --- pipeline_documentation.md | 42 +++++++++++++++++++-------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index 5f2a807..d698284 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -94,25 +94,25 @@ on installation and usage please see [here](README.md). | Name | License | Tag line | More info | | --- | --- | --- | --- | | **ASCII-style alignment pileups** | [Apache 2.0][license-apache2] | _"Generates ASCII-style pileups of read alignments in one or more BAM files for one or more genomic regions."_ | [code][code-ascii] | -| **BEDTools** | [GPLv2][license-gpl2] | _"[...] intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF"_ | [code][code-bedtools] / [manual][manual-bedtools] / [publication][pub-bedtools] | +| **BEDTools** | [GPLv2][license-gpl2] | _"[...] intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF"_ | [code][code-bedtools] / [manual][docs-bedtools] / [publication][pub-bedtools] | | **cufflinks** | [BSL-1.0][license-bsl1] | _"[...] assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples"_ | [code][code-cufflinks] / [manual][docs-cufflinks] / [publication][pub-cufflinks] | | **cutadapt** | [MIT][license-mit] | _"[...] finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads"_ | [code][code-cutadapt] / [manual][docs-cutadapt] / [publication][pub-cutadapt] | | **FASTX-Toolkit** | [AGPL-3.0][license-agpl3] | _"[...] collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing"_ | [code][code-fastx] / [manual][docs-fastx] | -| **GFFUtils** | [AFL-3][license-afl3] | _"[...] a small set of utility programs for working with GFF and GTF files"_ | [code][code-gffutils] / [manual][docs-gffutils] | +| **GFFUtils** | [AFL-3][license-afl3] | _"[...] a small set of utility programs for working with GFF and GTF files"_ | [code][code-gffutils] / [manual][docs-gffutils] | | **Oligomap** | [GPLv3][license-gpl3] | _"[...] fast identification of nearly-perfect matches of small RNAs in sequence databases. It allows to exhaustively identify all the perfect and 1-error (where an error is defined to be a mismatch, insertion or deletion) matches of large sets of small RNAs to target sequences"_ | [code][code-oligomap] / [publication][pub-oligomap] | | **SAMtools** | [MIT][license-mit] | _"[...] suite of programs for interacting with high-throughput sequencing data"_ | [code][code-samtools] / [manual][docs-samtools] / [publication][pub-samtools] | -| **segemehl** | [GPLv3][license-gpl3] | _"[...] map short sequencer reads to reference genomes"_ | [manual][docs-segemehl] / [publication][pub-segemehl] | +| **segemehl** | [GPLv3][license-gpl3] | _"[...] map short sequencer reads to reference genomes"_ | [manual][docs-segemehl] / [publication][pub-segemehl] | ## Description of workflow steps > The workflow consists of five Snakemake files: A main `Snakefile` and an -> individual Snakemake file for each step in the workflow (the genome resources -> preparation, the reads mapping, the miRNA quantification and the ASCII-style -> pileups generation). The main `Snakefile` contains the configuration file -> validation along with the inclusion of the sub-workflows. Individual steps of -> the workflow are described briefly along with some examples, and links to the -> respective software manuals are given. Parameters that can be modified by the -> user (via the samples table and the configuration file) are also described. +> individual Snakemake file each for the genome resources preparation, the +> reads mapping, the miRNA quantification and the ASCII-style pileups +> generation. The main `Snakefile` contains the configuration file validation +> along with the wiring of the modules. Individual steps of the workflow are +> described briefly along with some examples, and links to the respective +> software manuals are given. Parameters that can be modified by the user (via +> the samples table and the configuration file) are also described. ### Rule graph @@ -920,14 +920,14 @@ OUT: #### `filter_by_indels` -Filter multimappers favoring mismatches over indels with a +Filter multimappers favoring mismatches over InDels with a [**custom script**][custom-script-filter-mm]. -> Under the assumption that indels are less frequent than mismatches only +> Under the assumption that InDels are less frequent than mismatches only > those alignments (of the same read with the same edit distance) with the -> lowest number of indels are kept. This approach allows the presence of -> multimappers and/or indels after the filtering if the alignments contain the -> same proportion of mismatches vs. indels. +> lowest number of InDels are kept. This approach allows the presence of +> multimappers and/or InDels after the filtering if the alignments contain the +> same proportion of mismatches vs. InDels. - **Input** - Alignments file, sorted, filtered (`.sam`); from @@ -939,7 +939,7 @@ Filter multimappers favoring mismatches over indels with a - **Examples** ```console -Example 1 | Different proportion of mismatches vs. indels +Example 1 | Different proportion of mismatches vs. InDels IN: 1-1 16 19 77595 255 14M1D8M * 0 0 GCAGGAGAATCACTGATGTCAG * MD:Z:14^T2A1C3 NH:i:2 NM:i:3 XA:Z:Q XI:i:1 @@ -948,7 +948,7 @@ OUT: 1-1 16 19 77595 255 14M1D8M * 0 0 GCAGGAGAATCACTGATGTCAG * MD:Z:14^T2A1C3 NM:i:3 XA:Z:Q XI:i:1 NH:i:1 HI:i:1 -Example 2 | Equal proportion of mismatches vs. indels +Example 2 | Equal proportion of mismatches vs. InDels IN: 1-1 0 19 142777 255 15M1I5M * 0 0 GCTAGGTGGGAGGCTTGAAGC * MD:Z:4C0T14 NH:i:3 NM:i:3 XA:Z:Q XI:i:0 @@ -1197,7 +1197,7 @@ NEW TAG: YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 -Example 3 | Intersecting an isomiR (no indels nor mismatches) +Example 3 | Intersecting an isomiR (no InDels nor mismatches) IN miRNA annotations: chr19 . miRNA 5338 5359 . + . ID=MIMAT0005795;Alias=MIMAT0005795;Name=hsa-miR-1323;Derives_from=MI0003786 @@ -1247,7 +1247,7 @@ Tabulate alignments according to its new tag (`YW:Z`) with a > considered a canonical miRNA, which only keeps the annotated mature miRNA > name. A miRNA species is considered to be canonical if there are no shifts > between its start and end positions and the aligned read ones, and there -> are no mismatches nor indels. +> are no mismatches nor InDels. - **Input** - Alignments file, tagged, sorted (`.sam`); from @@ -1586,7 +1586,7 @@ libraries with [**ASCII-style alignment pileups**](#third-party-software-used). #### `create_per_run_ascii_pileups` Create ASCII-style pileups for all the desired annotated regions for the whole -run with [**ASCII-style alignment pilueups**](#third-party-software-used). +run with [**ASCII-style alignment pileups**](#third-party-software-used). > If no BED file is provided, the pileups' output directory will only contain > an empty file. @@ -1610,7 +1610,7 @@ run with [**ASCII-style alignment pilueups**](#third-party-software-used). Create ASCII-style pileups for all the desired annotated regions across the different library subsets if provided with -[**ASCII-style alignment pilueups**](#third-party-software-used). +[**ASCII-style alignment pileups**](#third-party-software-used). > **OPTIONAL RULE.** The ASCII-style pileups for each annotated region are > made if, and only if, at least one library subset is specified in the From 9030112658c751398015504efe11705923395b4a Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Wed, 15 May 2024 17:38:14 +0200 Subject: [PATCH 11/42] refactor: correct shift assessment --- scripts/iso_name_tagging.py | 110 ++++++++++++++++++------------------ 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index b2cb08b..52e059f 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -4,29 +4,29 @@ """Add intersecting feature(s) into a SAM file as a tag. -Build new names for the intersecting features from a BED file and add them as a -tag to alignments in a SAM file using the format -FEATURE_ID|5p-shift|3p-shift|CIGAR|MD. If either the BED or the SAM file is -empty, only the SAM file header is returned. +Build new names for the intersecting features from a BED file and add them as +a tag to alignments in a SAM file using the format +miRNA_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ. If either the BED or the SAM +file is empty, only the SAM file header is returned. EXPECTED INPUT FILES -The BED file must be the output a bedtools intersect call with -a being a GFF3 -file and -b a BAM file. If the GFF3 used in the bedtools intersect call has the -features start and end coordinates extended, the number of additional -nucleotides can be specified using the CLI option `--extension`. The SAM file -must contian only the reads that have an intersecting feature. +The BED file must be the output of a bedtools intersect call with `-a` being a +GFF3 file and `-b` a BAM file. If the GFF3 used in the bedtools intersect call +has the features start and end coordinates extended, the number of additional +nucleotides must be specified using the CLI option `--extension`. The SAM file +must contain only the reads that have an intersecting feature. NAME CREATION and TAG ADDITION -For each alignment, the name of the the intersecting feature will follow the -format FEATURE_ID|5p-shift|3p-shift|CIGAR|MD. The CLI option `--id` specifies -the feature identifier to be used as FEATURE_ID from within the attributes -column in the BED file. The 5p-shift and the 3-p shift values are the -difference between the feature start and end coordinates and the alignment -start and end coordinates. If `--extension` is provided, the feature start -position are adjusted by adding the given value and subtracting it from the -end position. If both, the 5p-shift and the 3p-shift, are within the range -+/- extension + 1 the feature name is added to the alignment as the new tag -"YW". Multiple intersecting feature names are separated by a semi-colon. +For each alignment, the name of the intersecting feature follows the +format miRNA_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ. The CLI option `--id` +specifies the feature identifier to be used as miRNA_ID from the attributes +column in the BED file. The 5' and 3' shift values are the difference between +the feature (extended) start and end coordinates and the alignment ones. If +`--extension` is provided, the feature start and end positions are adjusted by +adding and subtracting respectively the given value. If both, the 5' and +3'-end shifts, are within the range +/- extension (or equal 0 if no value is +provided) the feature name is added to the alignment as the new tag "YW". +Multiple intersecting feature names are separated by a semi-colon. EXAMPLES Example 1 @@ -37,9 +37,9 @@ command: iso_name_tagging.py -b BED -s SAM new name: - hsa-miR-524-5p|0|0|11M3I11M|22 + "" out SAM record: - 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 + 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: Example 2 in BED record: @@ -49,9 +49,9 @@ command: iso_name_tagging.py -b BED -s SAM new name: - "" + hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC out SAM record: - 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z: + 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC Example 3 in BED record: @@ -61,21 +61,21 @@ command: iso_name_tagging.py -b BED -s SAM --extension 6 new name: - hsa-miR-1323|0|-1|21M|21 + hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC out SAM record: - 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21 + 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC Example 4 in BED record: - 19 . miRNA 44377 44398 . + . ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160 19 44376 44398 13-1_1 1 + 22 + 19 . miRNA 44377 44404 . + . ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160 19 44376 44401 13-1_1 1 + 22 in SAM record: - 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 + 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:25 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 command: - iso_name_tagging.py -b BED -s SAM --id id + iso_name_tagging.py -b BED -s SAM --extension 6 --id id new name: - MIMAT0002849|0|0|11M3I11M|22 + MIMAT0002849|6|4|11M3I11M|25|CTACAAAGGGAGGTAGCACTTTCTC out SAM record: - 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002849|0|0|11M3I11M|22 + 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:25 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002849|6|4|11M3I11M|25|CTACAAAGGGAGGTAGCACTTTCTC """ # noqa: E501 # pylint: enable=line-too-long @@ -106,8 +106,8 @@ def parse_arguments(): "--bed", help=( "Path to the BED file. This file must be the output of " - " a bedtools intersect call with -a being a GFF3 file and" - " -b a BAM file." + " a bedtools intersect call with `-a` being a GFF3 file and" + " `-b` a BAM file." ), type=Path, required=True, @@ -143,7 +143,7 @@ def parse_arguments(): def attributes_dictionary(attr: str) -> Dict[str, str]: - """Create attributes dicctionary.""" + """Create attributes dictionary.""" pairs = attr.split(";") if len(pairs[0].split("=")) == 2: @@ -220,45 +220,45 @@ def parse_intersect_output( def get_tags( - intersecting_mirna: list, alignment: pysam.AlignedSegment, extension: int + intersecting_mirna: list, alignment: pysam.AlignedSegment, extend: int ) -> set: """Get tag for alignment. - Given an alignment and a list containing the feature name, start position, - and end position, create a list of strings to be added as a new tag to that - alignment. The string has the format: - feature-id|5p-shift|3p-shift|CIGAR|MD. The 5p-shift and 3p-shift are - calculated as a difference between the feature start/end position and the - alignment start/end position. If the start and end position of the - alignment differs at most by the extension argument value to the feature - start and end positions respectively, the name will be add to the final + Given an alignment and a list containing the name, start and end + (extended) positions of all the intersecting miRNA species, create the set + of strings used as a new custom tag to that alignment. + Each string follows the format: + miRNA_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ + The 5' end shift is computed as the difference between the feature and the + alignment positions. Similarly, the 3'-end shift is the result of + subtracting the feature end position to the alignment's one. If both shifts + values are within the range +/-extension, the name is added to the final list. Args: intersecting_mirna: - list with the feature name, start and end positions + list with the miRNA species name, start and end positions alignment: alignment to create the tag for - extension: - maximum number of nucleotides the alignment start and end positions - can differ from the feature to count it as an intersecting feature + extend: + value that sets the range in which both shifts have to be in to + create a new string for a particular miRNA species Returns: tags: - set of strings containing the new tag + set of strings for each valid intersecting miRNA """ cigar = alignment.cigarstring + seq = alignment.query_sequence md = alignment.get_tag("MD") - limit = extension + 1 tags = [] - for miRNA_name, miRNA_start, miRNA_end in intersecting_mirna: - shift_5p = alignment.reference_start - miRNA_start + 1 - shift_3p = alignment.reference_end - miRNA_end - - if -limit < shift_5p < limit and -limit < shift_3p < limit: - tags.append(f"{miRNA_name}|{shift_5p}|{shift_3p}|{cigar}|{md}") + for miR_name, miR_start, miR_end in intersecting_mirna: + shift_5 = alignment.reference_start - miR_start + 1 + shift_3 = alignment.reference_start + alignment.query_length - miR_end + if -extend <= shift_5 <= extend and -extend <= shift_3 <= extend: + tags.append(f"{miR_name}|{shift_5}|{shift_3}|{cigar}|{md}|{seq}") return set(tags) @@ -282,7 +282,7 @@ def main(arguments) -> None: tags = get_tags( intersecting_mirna=intersecting_miRNAs, alignment=alignment, - extension=arguments.extension, + extend=arguments.extension, ) alignment.set_tag("YW", ";".join(tags)) From f37af5292e11da84ffdbba0f389ffb87a6c0a4bb Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Fri, 24 May 2024 07:59:54 +0200 Subject: [PATCH 12/42] docs: update pipeline documentation --- pipeline_documentation.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index d698284..8289101 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -109,10 +109,11 @@ on installation and usage please see [here](README.md). > individual Snakemake file each for the genome resources preparation, the > reads mapping, the miRNA quantification and the ASCII-style pileups > generation. The main `Snakefile` contains the configuration file validation -> along with the wiring of the modules. Individual steps of the workflow are -> described briefly along with some examples, and links to the respective -> software manuals are given. Parameters that can be modified by the user (via -> the samples table and the configuration file) are also described. +> and imports the various functional modules described below. Individual steps +> of the workflow are described briefly along with some examples, and links to +> the respective software manuals are given. Parameters that can be modified by +> the user (via the samples table and the configuration file) are also +> described. ### Rule graph From dc5028e63506e5f1afa641434c904b21186d0c05 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Fri, 24 May 2024 08:00:11 +0200 Subject: [PATCH 13/42] docs: update README --- README.md | 39 ++++++++++++++++++++++++++++++++++----- 1 file changed, 34 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 2fec1ef..4d1de9b 100644 --- a/README.md +++ b/README.md @@ -323,36 +323,65 @@ snakemake \ ## Workflow description +_MIRFLOWZ_ consists of a main `Snakefile` and four functional modules. In the +`Snakefile`, the configuration file is validated, and the various modules are +imported. +The modules (1) process the genome resources, (2) map and (3) quantify the +reads, and (4) generate pileups, as described in detail below. + +> **NOTE:** For an elaborated description of each rule along with some +> examples, please, refer to the +> [workflow documentation](pipeline_documentation.md). + + +### Prepare module + The _MIRFLOWZ_ workflow initially processes and indexes the genome resources provided by the user. The regions corresponding to mature miRNAs are extended by a fixed but user-adjustable number of nucleotides on both sides to accommodate isomiR species with shifted start and/or end positions. If necessary, pri-miR loci are extended to adjust to the new miRNA coordinates. + +### Map module + The user-provided short-read small RNA-seq libraries undergo quality filtering (skipped if libraries are provided in FASTA rather than FASTQ), followed by adapter removal. The resulting reads are independently mapped to both the genome and the transcriptome using two distinct aligners: Segemehl and our in-house tool -Oligomap. On the one hand, Segemehl implements a fast heuristic strategy that +Oligomap. + +On the one hand, Segemehl implements a fast heuristic strategy that returns the alignment(s) with the smallest edit distance. Oligomap, on the other hand, implements a slower and more restricted approach that reports all the alignments with an edit distance of at most 1. The combination of the fast and flexible results and the strict selection ensures results with a higher -fidelity than if only one of the tools were to be used. After the mapping, +fidelity than if only one of the tools were to be used. + + +After the mapping, duplicate alignments resulting from the partially redundant mapping strategy are discarded and only the best alignments for each read are retained in a -a single file. +single file. + +### Quantify module + + +### ASCII-style pileups module + Finally, to visualize the distribution of read alignments around miRNA loci, ASCII-style alignment pileups are optionally generated for user-defined regions of interest. -> **NOTE:** For a detailed description of each rule along with some examples, -> please, refer to the [workflow documentation](pipeline_documentation.md). The schema below is a visual representation of the individual workflow steps and how they are related: From bbb07270aa911a91ec171e6816366b4504d11016 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Mon, 10 Jun 2024 17:29:52 +0200 Subject: [PATCH 14/42] fix typos2 --- scripts/iso_name_tagging.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index 52e059f..37d3dac 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -157,7 +157,7 @@ def attributes_dictionary(attr: str) -> Dict[str, str]: def parse_intersect_output( - intersect_file: Path, ID: str = "name", extension: int = 0 + intersect_file: Path, id: str = "name", extension: int = 0 ) -> Optional[Dict[Optional[str], list]]: """Parse intersect BED file. @@ -205,7 +205,7 @@ def parse_intersect_output( for line in bedfile: fields = Fields(*line.strip().split("\t")) - miRNA_name = attributes_dictionary(fields.feat_attributes)[ID] + miRNA_name = attributes_dictionary(fields.feat_attributes)[id] miRNA_start = int(fields.feat_start) + extension miRNA_end = int(fields.feat_end) - extension @@ -263,13 +263,15 @@ def get_tags( return set(tags) -def main(arguments) -> None: +def main(args) -> None: """Add intersecting feature(s) into a SAM file as a tag.""" intersect_data = parse_intersect_output( - arguments.bed, arguments.id, arguments.extension + intersect_file=args.bed, + id=args.id, + extension=args.extension, ) - with pysam.AlignmentFile(arguments.sam, "r") as samfile: + with pysam.AlignmentFile(args.sam, "r") as samfile: sys.stdout.write(str(samfile.header)) if intersect_data is None: @@ -282,7 +284,7 @@ def main(arguments) -> None: tags = get_tags( intersecting_mirna=intersecting_miRNAs, alignment=alignment, - extend=arguments.extension, + extend=args.extension, ) alignment.set_tag("YW", ";".join(tags)) @@ -290,5 +292,5 @@ def main(arguments) -> None: if __name__ == "__main__": - args = parse_arguments().parse_args() # pragma: no cover - main(args) # pragma: no cover + arguments = parse_arguments().parse_args() # pragma: no cover + main(arguments) # pragma: no cover From c1bc82c5ab1b0820cc8792ca3afbf49daad75d81 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Mon, 17 Jun 2024 08:15:12 +0200 Subject: [PATCH 15/42] docs: extend workflow description --- README.md | 125 +++++++++++++++++++++++++++++++++--------------------- 1 file changed, 76 insertions(+), 49 deletions(-) diff --git a/README.md b/README.md index 4d1de9b..5a03d9f 100644 --- a/README.md +++ b/README.md @@ -15,6 +15,10 @@ _MIRFLOWZ_ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs. - [Expected output files](#expected-output-files) - [Creating a Snakemake report](#creating-a-snakemake-report) 3. [Workflow description](#workflow-description) + - [Prepare module](#prepare-module) + - [Map module](#map-module) + - [Quantify module](#quantify-module) + - [ASCII-style pileups module](#ascii-style-pileups-module) 4. [Contributing](#contributing) 5. [License](#license) 6. [Contact](#contact) @@ -40,8 +44,8 @@ For improved reproducibility and reusability of the workflow, as well as an easy means to run it on a high performance computing (HPC) cluster managed, e.g., by [Slurm][slurm], all steps of the workflow run inside isolated environments ([Singularity][singularity] containers or [Conda][conda] -environments). As a consequence, running this workflow has only a few individual -dependencies. These are managed by the package manager Conda, which +environments). As a consequence, running this workflow has only a few +individual dependencies. These are managed by the package manager Conda, which needs to be installed on your system before proceeding. If you do not already have Conda installed globally on your system, @@ -210,8 +214,8 @@ There are 4 files you must provide: expected format. 5. **OPTIONAL**: A **BED6** file with regions for which to produce - [ASCII-style alignment pileups][ascii-pileups]. If not provided, no pileups - will be generated. See [here][bed-format] for the expected format. + [ASCII-style pileups][ascii-pileups]. If not provided, no pileups are + generated. See [here][bed-format] for the expected format. > General note: If you want to process the genome resources before use (e.g., > filtering), you can do that, but make sure the formats of any modified @@ -325,14 +329,22 @@ snakemake \ _MIRFLOWZ_ consists of a main `Snakefile` and four functional modules. In the `Snakefile`, the configuration file is validated, and the various modules are -imported. -The modules (1) process the genome resources, (2) map and (3) quantify the -reads, and (4) generate pileups, as described in detail below. - -> **NOTE:** For an elaborated description of each rule along with some -> examples, please, refer to the -> [workflow documentation](pipeline_documentation.md). - +imported. In addition, a handler for both, a successful and a failed run are +set. If the workflow finishes without any errors, all the intermediate files +are removed, otherwise, a log file is created. To keep the intermediate files +upon completion, use the `--no-hooks` CLI argument when running the pipeline. + +The modules [(1)](#prepare-module) process the genome resources, +[(2)](#map-module) map and [(3)](#quantify-module) quantify the reads, and +[(4)](#ascii-style-pileups-module) generate pileups, as described in detail +below. + +> **NOTE:** _MIRFLOWZ_ uses the notation provided by miRBase (_i.e._ +> "miRNA primary transcript" for precursors and "miRNA" for the canonical +> mature miRNA). This implies that precursors are named "pri-miRs" across the +> workflow instead of pre-miR. This decision is made upon the lack of +> guarantee that "miRNA primary transcripts" are full pre-miR (and pre-miR +> only) sequences. ### Prepare module @@ -342,35 +354,24 @@ by a fixed but user-adjustable number of nucleotides on both sides to accommodate isomiR species with shifted start and/or end positions. If necessary, pri-miR loci are extended to adjust to the new miRNA coordinates. + ### Map module The user-provided short-read small RNA-seq libraries undergo quality filtering (skipped if libraries are provided in FASTA rather than FASTQ), followed by -adapter removal. +adapter removal. The resulting reads are independently mapped to both the +genome and the transcriptome using two distinct aligners: Segemehl and our +in-house tool Oligomap. -The resulting reads are independently mapped to both the genome and the -transcriptome using two distinct aligners: Segemehl and our in-house tool -Oligomap. - -On the one hand, Segemehl implements a fast heuristic strategy that -returns the alignment(s) with the smallest edit distance. Oligomap, on the -other hand, implements a slower and more restricted approach that reports all -the alignments with an edit distance of at most 1. The combination of the fast -and flexible results and the strict selection ensures results with a higher -fidelity than if only one of the tools were to be used. - - -After the mapping, -duplicate alignments resulting from the partially redundant mapping strategy -are discarded and only the best alignments for each read are retained in a -single file. +Segemehl implements a fast heuristic strategy that returns the alignment(s) +with the smallest edit distance. Oligomap, on the other hand, implements a +slower and more restricted approach that reports all the alignments with an +edit distance of at most 1. The combination of the fast and flexible results +and the strict selection ensures results with a higher fidelity than if only +one of the tools was to be used. -### Quantify module +Two merging steps are done in order to have all the alignments in a single +file. In the first one, the transcriptome and the genome mappings from both +aligners are fused and only those alignments with a smaller NH than the one +provided are kept. For the second step, transcriptomic coordinates are turned +into genomic ones and alignments are combined into a single file. Duplicate +alignments resulting from the partially redundant mapping strategy are +discarded and only the best alignments for each read are retained (_i.e._ the +ones with the smallest edit distance). In addition, and due to the alignment's +aggregation, a second filtering according to the new NH is performed. + +A final filter is made to further increase the classification accuracy and +reduce the amount of multimappers. Given that isomiRs are known to present more +mismatches than InDels when compared to the canonical sequence they come from, +when addressing the multiple genomic locations a read has been mapped to, the +alignments with fewer InDels are kept. Note that some multimappers might still +be present if the number of InDels and mismatches is the same across +alignments. - +#### isomiRs notation + +A sequence is considered to be an isomiR if it has a shift on either end, an +InDel or a mismatch on its sequence when compared to the canonical miRNA it +maps and intersects with. + +_MIRFLOWZ_ employs an unambiguous notation to classify isomiRs using the +format `miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and +`3p-shift` represent the differences between the annotated mature miRNA +start and end positions and those of the read alignment, respectively. ### ASCII-style pileups module @@ -411,6 +437,10 @@ and how they are related: > ![rule-graph][rule-graph] +> **NOTE:** For an elaborated description of each rule along with some +> examples, please, refer to the +> [workflow documentation](pipeline_documentation.md). + ## Contributing _MIRFLOWZ_ is an open-source project which relies on community contributions. @@ -433,7 +463,6 @@ For questions or suggestions regarding the code, please use the [ascii-pileups]: [bed-format]: -[bedtools]: [chrMap]: [conda]: [cluster execution]: @@ -443,9 +472,7 @@ For questions or suggestions regarding the code, please use the [mamba]: [miniconda-installation]: [mirbase]: -[oligomap]: [rule-graph]: images/rule_graph.svg -[segemehl]: [singularity]: [slurm]: [snakemake]: From 26d78130bd3781c7a5da4cb4daed64b49e934a1d Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 28 Jul 2024 13:45:27 +0200 Subject: [PATCH 16/42] refactor: account for new notation --- scripts/mirna_quantification.py | 139 ++++++++++++++++---------------- 1 file changed, 68 insertions(+), 71 deletions(-) diff --git a/scripts/mirna_quantification.py b/scripts/mirna_quantification.py index 9f4ed88..4b13de6 100755 --- a/scripts/mirna_quantification.py +++ b/scripts/mirna_quantification.py @@ -9,7 +9,7 @@ covering the main modes. EXPECTED INPUT -The SAM file must contain only the alignments that interesct with canonical +The SAM file must contain only the alignments that intersect with canonical miRNAs and/or isomiRs. For each alignment, the intersecting feature name(s) must be stored in a tag. If the tag determined by the CLI argument `--tag` is empty, the alignment is ignored. In addition, the SAM file must be sorted by @@ -20,14 +20,15 @@ FEATURE NAME FORMAT The name of the intersecting feature(s) has to follow the format: -feat_name|5p-shift|3p-shift|CIGAR|MD. -For isomirs, the whole name is used. For canonical miRNAs, the `feat_name`. +feat_name|5p-shift|3p-shift|CIGAR|MD|READ_SEQ. +For isomiRs, the whole name is used. For canonical miRNAs, the `feat_name`. A feature is classified as canonical if the 5p and 3p shifts are both 0 and the CIGAR and MD strings are the same. If there are different features names -separated by a semi-colon, they are treated as a unique isomir name. For -example, the feature name 'feat_name_1|0|0|23M|23' would represent a canonical -miRNA and the feature names 'feat_name_2|0|0|22M|0A0A2T17' and -'feat_name_3|0|0|22M|22;feat_name_4|1|0|23M|17A3T0C0' would represent isomiRs. +separated by a semi-colon, they are treated as a unique isomiR name. For +example, the feature name 'feat_name_1|0|0|23M|23|read_seq' would represent +a canonical miRNA and the feature names 'feat_name_2|0|0|22M|0A0A2T17|read_seq' +and 'feat_name_3|0|0|22M|22|read_seq;feat_name_4|1|0|23M|17A3T0C0|read_seq' +would represent isomiRs. READ NAME FORMAT The read name must have one of the following formats: @@ -41,7 +42,7 @@ COUNT TABULATION The count for each feature is the sum of all the intersecting alignment's -contribution. The appropiate contribution is the ratio between the number of +contribution. The appropriate contribution is the ratio between the number of reads and the alignment's NH. The CLI flags `--collapsed` and `--nh` determine if these values are taken from the alignment's name. If `--collapsed` is not set, the number of reads is considered to be 1. If `--nh` is not set, the NH @@ -62,7 +63,7 @@ flags `--count`, `--len` and `--read-ids`. If `--count` is set, the output table will contain the number of best alignments for each feature. If `--len` is set, the output table will contain the read's length. If both `--count` and -`--len` are set, the count will always be followed by the read's lenght. If +`--len` are set, the count will always be followed by the read's length. If `--read-ids` is set, a semicolon-separated list of all alignment IDs that overlap with the feature will always be in the last column. @@ -71,7 +72,7 @@ input: SAM with intersecting feature names in stored in the tag XN command: mirna_quantification.py SAM --tag XN output: hsa-miR-516b-5p 3.0 - hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 + hsa-miR-517-5p|-1|0|23M|22T|ACCTCTAGATGGAAGCACTGTCG 0.6000000000000001 Example 2 input: SAM meeting the minimal characteristics @@ -82,26 +83,26 @@ Example 3 input: SAM meeting the minimal characteristics command: mirna_quantification.py SAM --mir-list isomir - output: hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 - hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 + output: hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTAA 1.6666666666666665 + hsa-miR-517-5p|-1|0|23M|22T|ACCTCTAGATGGAAGCACTGTCG 0.6000000000000001 Example 4 input: SAM with read names following the format NAME-COUNT_NH command: mirna_quantification.py SAM --collpased --nh output: hsa-miR-516b-5p 3.0 - hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 + hsa-miR-517-5p|-1|0|23M|22T|ACCTCTAGATGGAAGCACTGTCG 0.6000000000000001 Example 5 input: SAM with read names following the format NAME-COUNT command: mirna_quantification.py SAM --collapsed output: hsa-miR-516b-5p 3.0 - hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 + hsa-miR-517-5p|-1|0|23M|22T|ACCTCTAGATGGAAGCACTGTCG 0.6000000000000001 Example 6 input: SAM with read names following the format NAME_NH command: mirna_quantification.py SAM --nh output: hsa-miR-516b-5p 3.0 - hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 + hsa-miR-517-5p|-1|0|23M|22T|ACCTCTAGATGGAAGCACTGTCG 0.6000000000000001 Example 7 input: SAM with read names following the format NAME_NH @@ -112,8 +113,8 @@ Example 8 input: SAM meeting the minimal characteristics command: mirna_quantification.py SAM --count --len --mir-list isomir - output: hsa-miR-512-3p|0|1|23M|22C0 4.333333333333333 6 23 - hsa-miR-512-3p|0|1|23M|3T18C0 12.0 8 19 + output: hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTAA 4.333333333333333 6 23 + hsa-miR-512-3p|0|1|23M|3T18C0|AAGGGCTGTCATAGCTGAGGTAA 12.0 8 19 """ import argparse @@ -183,12 +184,12 @@ def parse_arguments(): "--collapsed", help=( "Indicate that the SAM file has the reads collapsed by sequence." - "In that case, the SAM query names are expected to follow the " - "format NAME-COUNT where NAME is an aribitrary unique name and " - "COUNT is is the number of identical reads that were collapsed " - "i.e my_query_name-13. The required naming format is produced, " - "e.g., by the 'fastx_collapser' tool of the " - "FASTX-Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/" + " In that case, the SAM query names are expected to follow the" + " format NAME-COUNT where NAME is an aribitrary unique name and" + " COUNT is is the number of identical reads that were collapsed" + " i.e my_query_name-13. The required naming format is produced," + " e.g., by the 'fastx_collapser' tool of the" + " FASTX-Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/" " Default: %(default)s." ), action="store_true", @@ -227,8 +228,9 @@ def parse_arguments(): parser.add_argument( "--read-ids", help=( - "If set, the read IDs that belong to each miRNA are included in " - "the output table separated by a semi-colon. Default: %(default)s." + "If set, the read IDs that belong to each miRNA are included in" + " the output table separated by a semi-colon." + " Default: %(default)s." ), action="store_true", default=False, @@ -242,7 +244,7 @@ def collapsed_nh_contribution(aln: pysam.AlignedSegment) -> float: The contribution is computed as the ratio of the number of reads collapsed in the alignment and the NH value. It is assumed that the alignment query - name contians the number of collapsed reads as well as the NH value in the + name contains the number of collapsed reads as well as the NH value in the format NAME-COUNT_NH. Args: @@ -250,7 +252,7 @@ def collapsed_nh_contribution(aln: pysam.AlignedSegment) -> float: Alignment to which the overall contribution is calculated Returns: - the conrtibution of the alignment to the overall count + The contribution of the alignment to the overall count """ name = str(aln.query_name) try: @@ -274,7 +276,7 @@ def collapsed_contribution(aln: pysam.AlignedSegment) -> float: The contribution is computed as the ratio of the number of reads collapsed in the alignment and the value stored in the NH tag. If the tag is missing, - the NH value is 1. It is assumed that the alignment query name contians + the NH value is 1. It is assumed that the alignment query name contains the number of collapsed reads in the format NAME-COUNT. Args: @@ -282,22 +284,20 @@ def collapsed_contribution(aln: pysam.AlignedSegment) -> float: Alignment to which the overall contribution is calculated Returns: - the conrtibution of the alignment to the overall count + The contribution of the alignment to the overall count """ name = str(aln.query_name) try: if coll := re.search(r"\d+$", name): collapsed = float(coll.group()) - except AttributeError: - sys.stdout.write( - f"Invalid query name: '{aln.query_name}'.\n" - + "Option --collapsed specified but query name does" - + " not include the number of collapsed sequences.\n" - + "Check SAM file consistency and CLI options" - + " --collapsed and --nh.\n" - ) - raise + except AttributeError as atterr: + raise AttributeError( + f'Invalid query name: "{aln.query_name}".\n' + f"Option --collapsed specified but query name does not include" + f" the number of collapsed sequences.\nCheck SAM file consistency" + f" and CLI options --collapsed and --nh." + ) from atterr try: nh_value = float(aln.get_tag("NH")) @@ -312,7 +312,7 @@ def nh_contribution(aln: pysam.AlignedSegment) -> float: The contribution is computed as the ratio of the number of reads collapsed in the alignment and the value stored in the NH tag. If the tag is missing, - the NH value is 1. It is assumed that the alignment query name contians the + the NH value is 1. It is assumed that the alignment query name contains the NH value in the format NAME_NH. Args: @@ -320,7 +320,7 @@ def nh_contribution(aln: pysam.AlignedSegment) -> float: Alignment to which the overall contribution is calculated Returns: - the conrtibution of the alignment to the overall count + The contribution of the alignment to the overall count """ name = str(aln.query_name) try: @@ -329,15 +329,12 @@ def nh_contribution(aln: pysam.AlignedSegment) -> float: return 1 / nh_val - except AttributeError: - sys.stdout.write( - f"Invalid query name: '{aln.query_name}'.\n" - + "Option --nh specified but query name does" - + " not include NH.\n" - + "Check SAM file consistency and CLI options" - + " --collapsed and --nh.\n" - ) - raise + except AttributeError as atterr: + raise AttributeError( + f'Invalid query name: "{aln.query_name}".\n' + f"Option --nh specified but query name does not include NH.\n" + f"Check SAM file consistency and CLI options --collapsed and --nh." + ) from atterr def contribution(aln: pysam.AlignedSegment) -> float: @@ -352,7 +349,7 @@ def contribution(aln: pysam.AlignedSegment) -> float: Alignment to which the overall contribution is calculated Returns: - the conrtibution of the alignment to the overall count + The contribution of the alignment to the overall count """ try: return 1 / float(aln.get_tag("NH")) @@ -362,7 +359,7 @@ def contribution(aln: pysam.AlignedSegment) -> float: def get_name(pre_name: str) -> list[str]: - """Get the final name for the spieces name. + """Get the final name for the species name. Take a string and processes it to obtain the final name for the species and the type of miRNA the string belongs to. Only the feat_name is @@ -397,11 +394,11 @@ def write_output( mirna.write("") -def main(arguments) -> None: +def main(args) -> None: """Quantify miRNAs and corresponding isomiRs.""" - outdir = Path(arguments.outdir) + outdir = Path(args.outdir) outdir.mkdir(parents=True, exist_ok=True) - outfile = outdir / f"mirna_counts_{arguments.lib}" + outfile = outdir / f"mirna_counts_{args.lib}" contribution_type = { (True, True): collapsed_nh_contribution, @@ -410,12 +407,12 @@ def main(arguments) -> None: (False, False): contribution, } - get_contribution = contribution_type[arguments.collapsed, arguments.nh] + get_contribution = contribution_type[args.collapsed, args.nh] - with pysam.AlignmentFile(arguments.samfile, "r") as samfile: + with pysam.AlignmentFile(args.samfile, "r") as samfile: try: alignment = next(samfile) - current_species = alignment.get_tag(arguments.tag) + current_species = alignment.get_tag(args.tag) if current_species: read_ID = [str(alignment.query_name)] count = get_contribution(alignment) @@ -425,7 +422,7 @@ def main(arguments) -> None: write_output( name="", species=[], - mir_list=arguments.mir_list, + mir_list=args.mir_list, mirna_out=outfile, ) @@ -433,14 +430,14 @@ def main(arguments) -> None: for alignment in samfile: if current_species == "": - current_species = alignment.get_tag(arguments.tag) + current_species = alignment.get_tag(args.tag) count = get_contribution(alignment) alns_count = 1 read_ID = [str(alignment.query_name)] continue - if current_species == alignment.get_tag(arguments.tag): + if current_species == alignment.get_tag(args.tag): count += get_contribution(alignment) alns_count += 1 read_ID.append(str(alignment.query_name)) @@ -449,21 +446,21 @@ def main(arguments) -> None: name = get_name(str(current_species)) species = [name[1], str(count)] - if arguments.count: + if args.count: species.append(str(alns_count)) - if arguments.len: + if args.len: species.append(str(alignment.query_alignment_length)) - if arguments.read_ids: + if args.read_ids: species.append(";".join(read_ID)) write_output( name=name[0], species=species, - mir_list=arguments.mir_list, + mir_list=args.mir_list, mirna_out=outfile, ) - current_species = alignment.get_tag(arguments.tag) + current_species = alignment.get_tag(args.tag) count = get_contribution(alignment) alns_count = 1 read_ID = [str(alignment.query_name)] @@ -471,21 +468,21 @@ def main(arguments) -> None: name = get_name(str(current_species)) species = [name[1], str(count)] - if arguments.count: + if args.count: species.append(str(alns_count)) - if arguments.len: + if args.len: species.append(str(alignment.query_alignment_length)) - if arguments.read_ids: + if args.read_ids: species.append(";".join(read_ID)) write_output( name=name[0], species=species, - mir_list=arguments.mir_list, + mir_list=args.mir_list, mirna_out=outfile, ) if __name__ == "__main__": - args = parse_arguments().parse_args() # pragma: no cover - main(args) # pragma: no cover + arguments = parse_arguments().parse_args() # pragma: no cover + main(arguments) # pragma: no cover From b57a5aae20e9da62d4c2771bafbf1a692c53547b Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 15:40:59 +0200 Subject: [PATCH 17/42] docs: complete documentation --- pipeline_documentation.md | 148 +++++++++++++++++++++++++++++--------- 1 file changed, 113 insertions(+), 35 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index 8289101..7e1c6c2 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -365,10 +365,18 @@ Extract chromosome(s) length from the genome sequence. #### `extend_mirs_annotations` -Extend miRNA annotations and split the file by feature with a -[**custom script**][custom-script-mir-ext]. - -> Mature miRNA regions are extended on both sides to account for isomiR species +Extend miRNA annotations, ensure feature names uniqueness and split the file +by feature with a [**custom script**][custom-script-mir-ext]. + +> Adjust miRNAs' 'Name' attribute to account for the different genomic +> locations the miRNA sequence is annotated on and ensure their uniqueness. +> The name format is `SPECIES-mir-NAME-#` for pri-miRs, and +> `SPECIES-miR-NAME-#-ARM` or `SPECIES-miR-NAME-#` for mature miRNA with both +> or just one arm respectively, where `#` is the replica integer. If a pri-miR +> has a replica but its number is set in the 'ID' attribute, the first instance +> does not has a suffix but the other one(s) do. If a precursor has no other +> occurrences, no further modifications are made. On the other hand, +> mature miRNA regions are extended on both sides to account for isomiR species > with shifted start and/or end positions without exceeding chromosome(s) > boundaries. If required, pri-miR loci are also extended to accommodate the > new miRNA coordinates. In addition, pri-miR names are modified to record the @@ -390,7 +398,7 @@ Extend miRNA annotations and split the file by feature with a - **Examples** ```console -Example 1 | Mature miRNA extension +Example 1 | Extension | Mature miRNA extension IN: pri-miR entry: @@ -403,10 +411,10 @@ OUT: pri-miR entry: 19 . miRNA_primary_transcript 2517 2614 . + . ID=MI0003141;Alias=MI0003141;Name=hsa-mir-512-2_-0_+0 mature miRNA entry: - 19 . miRNA 2530 2564 . + . ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003141 + 19 . miRNA 2530 2564 . + . ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-2-5p;Derives_from=MI0003141 -Example 2 | Mature miRNA and pri-miR extension +Example 2 | Extension | Mature miRNA and pri-miR extension IN: pri-miR entry: @@ -417,12 +425,12 @@ IN: 6 OUT: pri-miR entry: - 19 . miRNA_primary_transcript 6 124 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-3_+2 + 19 . miRNA_primary_transcript 6 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-3_+0 mature miRNA entry: - 19 . miRNA 6 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 + 19 . miRNA 6 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-1-5p;Derives_from=MI0003140 -Example 3 | Matrue miRNA exceeding chromosome boundaries extension +Example 3 | Extension | Matrue miRNA exceeding chromosome boundaries extension IN: pri-miR entry: @@ -433,9 +441,71 @@ IN: 6 OUT: pri-miR entry: - 19 . miRNA_primary_transcript 0 124 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-2_+2 + 19 . miRNA_primary_transcript 1 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-1_+0 mature miRNA entry: - 19 . miRNA 0 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 + 19 . miRNA 1 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-1-5p;Derives_from=MI0003140 + + +Example 4 | Name uniqueness | Replica number in the ID + +IN: + pri-miR entries: + chr21 . miRNA_primary_transcript 8206563 8206618 . + . ID=MI0033425;Alias=MI0033425;Name=hsa-mir-10401 + chr21 . miRNA_primary_transcript 8250772 8250827 . + . ID=MI0033425_2;Alias=MI0033425;Name=hsa-mir-10401 + mature miRNA entries: + chr21 . miRNA 8206563 8206582 . + . ID=MIMAT0041633;Alias=MIMAT0041633;Name=hsa-miR-10401-5p;Derives_from=MI0033425 + chr21 . miRNA 8206598 8206618 . + . ID=MIMAT0041634;Alias=MIMAT0041634;Name=hsa-miR-10401-3p;Derives_from=MI0033425 + chr21 . miRNA 8250772 8250791 . + . ID=MIMAT0041633_1;Alias=MIMAT0041633;Name=hsa-miR-10401-5p;Derives_from=MI0033425 + chr21 . miRNA 8250807 8250827 . + . ID=MIMAT0041634_1;Alias=MIMAT0041634;Name=hsa-miR-10401-3p;Derives_from=MI0033425 +OUT: + pri-miR entries: + chr21 . miRNA_primary_transcript 8206563 8206618 . + . ID=MI0033425;Alias=MI0033425;Name=hsa-mir-10401 + chr21 . miRNA_primary_transcript 8250772 8250827 . + . ID=MI0033425_2;Alias=MI0033425;Name=hsa-mir-10401-2 + mature miRNA entries: + chr21 . miRNA 8206563 8206582 . + . ID=MIMAT0041633;Alias=MIMAT0041633;Name=hsa-miR-10401-5p;Derives_from=MI0033425 + chr21 . miRNA 8206598 8206618 . + . ID=MIMAT0041634;Alias=MIMAT0041634;Name=hsa-miR-10401-3p;Derives_from=MI0033425 + chr21 . miRNA 8250772 8250791 . + . ID=MIMAT0041633_1;Alias=MIMAT0041633;Name=hsa-miR-10401-2-5p;Derives_from=MI0033425 + chr21 . miRNA 8250807 8250827 . + . ID=MIMAT0041634_1;Alias=MIMAT0041634;Name=hsa-miR-10401-2-3p;Derives_from=MI0033425 + + +Example 5 | Name uniqueness | Replica number in the Name; single mature arm + +IN: + pri-miR entries: + chr21 . miRNA_primary_transcript 8205315 8205406 . + . ID=MI0022559;Alias=MI0022559;Name=hsa-mir-6724-1 + chr21 . miRNA_primary_transcript 8249505 8249596 . + . ID=MI0031516;Alias=MI0031516;Name=hsa-mir-6724-2 + mature miRNA entries: + chr21 . miRNA 8205325 8205347 . + . ID=MIMAT0025856;Alias=MIMAT0025856;Name=hsa-miR-6724-5p;Derives_from=MI0022559 + chr21 . miRNA 8249515 8249537 . + . ID=MIMAT0025856_1;Alias=MIMAT0025856;Name=hsa-miR-6724-5p;Derives_from=MI0031516 +OUT: + pri-miR entries: + chr21 . miRNA_primary_transcript 8205315 8205406 . + . ID=MI0022559;Alias=MI0022559;Name=hsa-mir-6724-1 + chr21 . miRNA_primary_transcript 8249505 8249596 . + . ID=MI0031516;Alias=MI0031516;Name=hsa-mir-6724-2 + mature miRNA entries: + chr21 . miRNA 8205325 8205347 . + . ID=MIMAT0025856;Alias=MIMAT0025856;Name=hsa-miR-6724-1-5p;Derives_from=MI0022559 + chr21 . miRNA 8249515 8249537 . + . ID=MIMAT0025856_1;Alias=MIMAT0025856;Name=hsa-miR-6724-2-5p;Derives_from=MI0031516 + + +Example 6 | Name uniqueness | Both mature miRNA arms but just one with the replica number + +IN: + pri-miR entries: + chr2 . miRNA_primary_transcript 135665397 135665478 . + . ID=MI0000447;Alias=MI0000447;Name=hsa-mir-128-1 + chr3 . miRNA_primary_transcript 35744476 35744559 . + . ID=MI0000727;Alias=MI0000727;Name=hsa-mir-128-2 + mature miRNA entries: + chr2 . miRNA 135665446 135665466 . + . ID=MIMAT0000424;Alias=MIMAT0000424;Name=hsa-miR-128-3p;Derives_from=MI0000447 + chr2 . miRNA 135665411 135665433 . + . ID=MIMAT0026477;Alias=MIMAT0026477;Name=hsa-miR-128-1-5p;Derives_from=MI0000447 + chr3 . miRNA 35744527 35744547 . + . ID=MIMAT0000424_1;Alias=MIMAT0000424;Name=hsa-miR-128-3p;Derives_from=MI0000727 + chr3 . miRNA 35744490 35744512 . + . ID=MIMAT0031095;Alias=MIMAT0031095;Name=hsa-miR-128-2-5p;Derives_from=MI0000727 +OUT: + pri-miR entries: + chr2 . miRNA_primary_transcript 135665397 135665478 . + . ID=MI0000447;Alias=MI0000447;Name=hsa-mir-128-1 + chr3 . miRNA_primary_transcript 35744476 35744559 . + . ID=MI0000727;Alias=MI0000727;Name=hsa-mir-128-2 + mature miRNA entries: + chr2 . miRNA 135665446 135665466 . + . ID=MIMAT0000424;Alias=MIMAT0000424;Name=hsa-miR-128-1-3p;Derives_from=MI0000447 + chr2 . miRNA 135665411 135665433 . + . ID=MIMAT0026477;Alias=MIMAT0026477;Name=hsa-miR-128-1-5p;Derives_from=MI0000447 + chr3 . miRNA 35744527 35744547 . + . ID=MIMAT0000424_1;Alias=MIMAT0000424;Name=hsa-miR-128-2-3p;Derives_from=MI0000727 + chr3 . miRNA 35744490 35744512 . + . ID=MIMAT0031095;Alias=MIMAT0031095;Name=hsa-miR-128-2-5p;Derives_from=MI0000727 ``` ### Map workflow @@ -649,9 +719,11 @@ with a [**custom script**][custom-script-blocksort]. Convert aligned reads `.oligomap` to `.sam` and filter alignments by number of hits with a [**custom script**][custom-script-oligo-sam]. -> Given the short length of the reads and the sequence similarity among miRNAs, -> the number of hits can be notably high. Therefore, reads aligned beyond a -> specified value are disregarded. +> If a read has been aligned beyond a specified threshold, it is removed due +> to (1) performance reasons as the file size can rapidly increase, and (2) +> the fact that each read contributes to each count `1/N` where `N` is the +> number of genomic loci it aligns to and a large `N` makes the contribution +> negligible. - **Input** - Alignments file, sorted (`.oligomap`); from @@ -701,9 +773,11 @@ with a [**custom script**][custom-script-blocksort]. Convert aligned reads `.oligomap` to `.sam` and filter alignments by number of hits with a [**custom script**][custom-script-oligo-sam]. -> Given the short length of the reads and the sequence similarity among miRNAs, -> the number of hits can be notably high. Therefore, reads aligned beyond a -> specified value are disregarded. +> If a read has been aligned beyond a specified threshold, it is removed due +> to (1) performance reasons as the file size can rapidly increase, and (2) +> the fact that each read contributes to each count `1/N` where `N` is the +> number of genomic loci it aligns to and a large `N` makes the contribution +> negligible. - **Input** - Alignments file, sorted (`.oligomap`); from @@ -751,10 +825,11 @@ Concatenate [**segemehl**](#third-party-software-used) and Filter merged genome alignments by the number of hits with a [**custom script**][custom-script-nh-filter]. -> Given the short length of the reads, the sequence similarity among miRNAs, -> and the merging of two different mapping results, the number of hits can -> be notably high. Therefore, reads aligned beyond a specified value are -> disregarded. +> If a read has been aligned beyond a specified threshold, it is removed due +> to (1) performance reasons as the file size can rapidly increase, and (2) +> the fact that each read contributes to each count `1/N` where `N` is the +> number of genomic loci it aligns to and a large `N` makes the contribution +> negligible. - **Input** - Alignments file (`.sam`); from @@ -772,10 +847,11 @@ Filter merged genome alignments by the number of hits with a Filter merged transcriptome alignments by the number of hits with a [**custom script**][custom-script-nh-filter]. -> Given the short length of the reads, the sequence similarity among miRNAs, -> and the merging of two different mapping results, the number of hits can -> be notably high. Therefore, reads aligned beyond a specified value are -> disregarded. +> If a read has been aligned beyond a specified threshold, it is removed due +> to (1) performance reasons as the file size can rapidly increase, and (2) +> the fact that each read contributes to each count `1/N` where `N` is the +> number of genomic loci it aligns to and a large `N` makes the contribution +> negligible. - **Input** - Alignments file (`.sam`); from @@ -1441,13 +1517,16 @@ IN library 2 hsa-miR-1283 1 hsa-miR-1283|-1|-2|21M|21 1 +IN library 3 + ID lib_3 + OUT table - ID lib_1 lib_2 - hsa-miR-524-5p 1 1 - hsa-miR-524-5p|0|0|22M|9G12 1 NA - hsa-miR-524-5p|0|0|22M|9G9C2 1 NA - hsa-miR-1283 NA 1 - hsa-miR-1283|-1|-2|21M|21 NA 1 + ID lib_1 lib_2 lib_3 + hsa-miR-524-5p 1 1 NA + hsa-miR-524-5p|0|0|22M|9G12 1 NA NA + hsa-miR-524-5p|0|0|22M|9G9C2 1 NA NA + hsa-miR-1283 NA 1 NA + hsa-miR-1283|-1|-2|21M|21 NA 1 NA ``` @@ -1544,11 +1623,10 @@ Create an empty BED file if the user has not provided one. #### `compress_reference_genome` -Compress the processed genome with trimmed IDs using `bgzip`. +Compress the processed genome with trimmed IDs using `bgzip` with +[**SAMtools**](#third-party-software-used). > Required to perform the ASCII-style alignment pileups. -> In order to be able to use the `bgzip` command when running the workflow -> using Singularity, [**SAMtools**](#third-party-software-used) is used. - **Input** - Genome sequence, trimmed IDs (`.fa`); from From 774106553b7a6abb79f4c80a1288fda2c71d538e Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 15:41:13 +0200 Subject: [PATCH 18/42] docs: complete documentation --- README.md | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 5a03d9f..68a49f6 100644 --- a/README.md +++ b/README.md @@ -353,7 +353,11 @@ provided by the user. The regions corresponding to mature miRNAs are extended by a fixed but user-adjustable number of nucleotides on both sides to accommodate isomiR species with shifted start and/or end positions. If necessary, pri-miR loci are extended to adjust to the new miRNA coordinates. - +In addition, to account for the different genomic locations a miRNA sequence +can be annotated, the name of these sequences are modified to have the format +`SPECIES-mir-NAME-#` for pri-miRs and `SPECIES-miR-NAME-#-ARM` or +`SPECIES-miR-NAME-#` for mature miRNAs with both or just one arm respectively, +where `#` is the replica number. ### Map module @@ -370,15 +374,6 @@ edit distance of at most 1. The combination of the fast and flexible results and the strict selection ensures results with a higher fidelity than if only one of the tools was to be used. - - Two merging steps are done in order to have all the alignments in a single file. In the first one, the transcriptome and the genome mappings from both aligners are fused and only those alignments with a smaller NH than the one @@ -388,6 +383,10 @@ alignments resulting from the partially redundant mapping strategy are discarded and only the best alignments for each read are retained (_i.e._ the ones with the smallest edit distance). In addition, and due to the alignment's aggregation, a second filtering according to the new NH is performed. +If a read has been aligned beyond a specified threshold, it is removed due to +(1) performance reasons as the file size can rapidly increase, and (2) the fact +that each read contributes to each count `1/N` where `N` is the number of +genomic loci it aligns to and a large `N` makes the contribution negligible. A final filter is made to further increase the classification accuracy and reduce the amount of multimappers. Given that isomiRs are known to present more @@ -409,7 +408,7 @@ precursors, mature miRNA and/or isomiRs, and all library counts are fused into a single table. Note that an alignment is only counted towards a given miRNA (or isomiR) species if one of its alignments fully falls within the (previously extended) locus annotated for that miRNA. Specifically, reads -contribute with `1/n` for each miRNA for which that is the case, where `n` is +contribute with `1/N` for each miRNA for which that is the case, where `N` is the total number of genomic loci the read aligns to. Under this criterion, the precursor counts contain reads that intersect with its mature arm(s), its hairpin sequence and/or the whole precursor itself. From 694a537d0fa0688ca0f025dc24fc9c57d670435e Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 16:17:47 +0200 Subject: [PATCH 19/42] refactor: adapt script to new name format --- scripts/mirna_quantification.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/mirna_quantification.py b/scripts/mirna_quantification.py index bba5854..ef29e8c 100755 --- a/scripts/mirna_quantification.py +++ b/scripts/mirna_quantification.py @@ -20,7 +20,7 @@ FEATURE NAME FORMAT The name of the intersecting feature(s) has to follow the format: -feat_name|5p-shift|3p-shift|CIGAR|MD|READ_SEQ. +FEAT_NAME|5p-SHIFT|3p-SHIFT|CIGAR|MD|READ_SEQ. For isomiRs, the whole name is used. For canonical miRNAs, the `feat_name`. A feature is classified as canonical if the 5p and 3p shifts are both 0 and the CIGAR and MD strings are the same. If there are different features names @@ -69,7 +69,7 @@ EXAMPLES Example 1 - input: SAM with intersecting feature names in stored in the tag XN + input: SAM with intersecting feature names in the tag XN command: mirna_quantification.py SAM --tag XN output: hsa-miR-516b-5p 3.0 hsa-miR-517-5p|-1|0|23M|22T|ACCTCTAGATGGAAGCACTGTCG 0.6000000000000001 @@ -108,7 +108,7 @@ input: SAM with read names following the format NAME_NH command: mirna_quantification.py SAM --read-ids --nh --mir-list mirna output: hsa-miR-498-5p 4.333333333333333 270396_3 - hsa-miR-1323 12.0 673650_2;673650_2 + hsa-miR-1323 12.0 673650_2;906983_4 Example 8 input: SAM meeting the minimal characteristics @@ -372,7 +372,7 @@ def get_name(pre_name: str) -> list[str]: Args: pre_name: - string with the format feat_name|5p-shift|3p-shift|CIGAR|MD + string with the format FEAT_NAME|5p-SHIFT|3p-SHIFT|CIGAR|MD|READ_SEQ Returns: list with the species name to be found in the final table and its type From 177c7ae82e03c5b40a8e8291e490a799b2c95f33 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 19:34:47 +0200 Subject: [PATCH 20/42] refactor: add read seq to isomiR tag --- scripts/iso_name_tagging.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index 37d3dac..035cb1b 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -233,7 +233,8 @@ def get_tags( alignment positions. Similarly, the 3'-end shift is the result of subtracting the feature end position to the alignment's one. If both shifts values are within the range +/-extension, the name is added to the final - list. + list. Note that `pysam` assumes 0-base index therefore, the addition of + one base is required to compute the 5' end shift. Args: intersecting_mirna: From c578d9ebeff484cebf18527a8058a3231338fff0 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 19:35:26 +0200 Subject: [PATCH 21/42] test: update unit test files --- scripts/tests/files/mirna_tag.sam | 50 ++++++++--------- scripts/tests/files/mirna_tag_extension.sam | 60 ++++++++++----------- scripts/tests/files/mirna_tag_id.sam | 50 ++++++++--------- 3 files changed, 80 insertions(+), 80 deletions(-) diff --git a/scripts/tests/files/mirna_tag.sam b/scripts/tests/files/mirna_tag.sam index 97f55f2..3eac8be 100644 --- a/scripts/tests/files/mirna_tag.sam +++ b/scripts/tests/files/mirna_tag.sam @@ -3,32 +3,32 @@ @PG ID:samtools PN:samtools VN:1.16.1 CL:samtools sort -n -o results/test_lib/header_sorted_catMappings.sam results/test_lib/concatenated_header_catMappings.sam @PG ID:samtools.1 PN:samtools PP:samtools VN:1.16.1 CL:samtools view -H results/test_lib/removeMultimappers.sam @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:samtools view -H results/test_lib/premir_intersectedAlignments.sam -8-2_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-3p|0|0|21M|21 -13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 -14-1_1 0 19 7590 1 20M3I3M * 0 0 TTTCAAGCCAGGGGGCGTTTCCGTTC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|0|20M3I3M|23 -15-1_1 0 19 7590 255 23M * 0 0 TTTCAAGTCAGGGGGCGTTTTTC * MD:Z:7C15 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|23M|7C15 -20-1_1 0 19 7590 255 15M1D7M * 0 0 TTTCAAGCCAGGGGGGTTTTTC * MD:Z:15^C7 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|15M1D7M|15^C7 -22-1_1 0 19 5338 1 18M3I4M * 0 0 TCAAAACTGAGGGGCATTGGATTCT * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|0|18M3I4M|22 -24-1_1 0 19 44414 255 11M1I10M * 0 0 GAAGGCGCTTCACCTTTGGAGT * MD:Z:22 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|0|11M1I10M|22 -26-1_1 0 19 7626 255 7M1I16M * 0 0 AAAGCACTCTCCAGAGCTTGAAGC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|7M1I16M|24 -31-1_1 0 19 7626 255 8M1D14M * 0 0 AAAGCACCCCAGAGCTTGAAGC * MD:Z:8^T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|8M1D14M|8^T14 -32-1_1 0 19 7626 1 23M * 0 0 AAAGCACCTCTTGAGCTTGAAGC * HI:i:0 MD:Z:10C0A11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|0|23M|10C0A11 -33-1_1 0 19 44377 255 18M1I4M * 0 0 CTACAAAGGGAAGCACTTGTCTC * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|0|18M1I4M|23 -34-1_1 0 19 7590 1 23M * 0 0 TTTCAAGCCAGATGGCGTTTTTC * HI:i:0 MD:Z:11G0G10 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|0|23M|11G0G10 -39-1_1 0 19 7590 255 19M1I4M * 0 0 TTTCAAGCCAGGGGGCGTTATTTC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|19M1I4M|24 -41-1_1 0 19 5338 255 15M1I7M * 0 0 TCAAAACTGAGGGGCTATTTTCT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|0|15M1I7M|23 -44-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22 -46-1_1 0 19 5338 1 22M * 0 0 TCAAAACTGAGGGGCATGCTCT * HI:i:0 MD:Z:17T0T3 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|0|22M|17T0T3 +8-2_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-3p|0|0|21M|21|GAAGGCGCTTCCCTTTGGAGT +13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +14-1_1 0 19 7590 1 20M3I3M * 0 0 TTTCAAGCCAGGGGGCGTTTCCGTTC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +15-1_1 0 19 7590 255 23M * 0 0 TTTCAAGTCAGGGGGCGTTTTTC * MD:Z:7C15 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|23M|7C15|TTTCAAGTCAGGGGGCGTTTTTC +20-1_1 0 19 7590 255 15M1D7M * 0 0 TTTCAAGCCAGGGGGGTTTTTC * MD:Z:15^C7 NH:i:1 NM:i:1 YW:Z: +22-1_1 0 19 5338 1 18M3I4M * 0 0 TCAAAACTGAGGGGCATTGGATTCT * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +24-1_1 0 19 44414 255 11M1I10M * 0 0 GAAGGCGCTTCACCTTTGGAGT * MD:Z:22 NH:i:1 NM:i:1 YW:Z: +26-1_1 0 19 7626 255 7M1I16M * 0 0 AAAGCACTCTCCAGAGCTTGAAGC * MD:Z:24 NH:i:1 NM:i:1 YW:Z: +31-1_1 0 19 7626 255 8M1D14M * 0 0 AAAGCACCCCAGAGCTTGAAGC * MD:Z:8^T14 NH:i:1 NM:i:1 YW:Z: +32-1_1 0 19 7626 1 23M * 0 0 AAAGCACCTCTTGAGCTTGAAGC * HI:i:0 MD:Z:10C0A11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|0|23M|10C0A11|AAAGCACCTCTTGAGCTTGAAGC +33-1_1 0 19 44377 255 18M1I4M * 0 0 CTACAAAGGGAAGCACTTGTCTC * MD:Z:23 NH:i:1 NM:i:1 YW:Z: +34-1_1 0 19 7590 1 23M * 0 0 TTTCAAGCCAGATGGCGTTTTTC * HI:i:0 MD:Z:11G0G10 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|0|23M|11G0G10|TTTCAAGCCAGATGGCGTTTTTC +39-1_1 0 19 7590 255 19M1I4M * 0 0 TTTCAAGCCAGGGGGCGTTATTTC * MD:Z:24 NH:i:1 NM:i:1 YW:Z: +41-1_1 0 19 5338 255 15M1I7M * 0 0 TCAAAACTGAGGGGCTATTTTCT * MD:Z:23 NH:i:1 NM:i:1 YW:Z: +44-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22|TCAAAACTGAGGGGCATTTTCT +46-1_1 0 19 5338 1 22M * 0 0 TCAAAACTGAGGGGCATGCTCT * HI:i:0 MD:Z:17T0T3 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|0|22M|17T0T3|TCAAAACTGAGGGGCATGCTCT 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z: -49-1_1 0 19 7626 1 12M3I11M * 0 0 AAAGCACCTCCATTTGAGCTTGAAGC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|0|12M3I11M|23 -54-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23 -56-1_1 0 19 44377 1 22M * 0 0 CTACAAAGGTAAGCACTTTATC * HI:i:0 MD:Z:9G9C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|22M|9G9C2 -57-1_1 0 19 7626 255 23M * 0 0 AAAGCACCTCCAGAGCTTGAAGC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-3p|0|0|23M|23 -58-1_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCACTTTGGAGT * MD:Z:11C9 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|0|21M|11C9 -59-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|0|22M|22 -66-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGTGCATTTTCT * MD:Z:12G9 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|0|22M|12G9 -71-1_1 0 19 7626 255 23M * 0 0 AAAGCACCACCAGAGCTTGAAGC * MD:Z:8T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|23M|8T14 -72-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGTAAGCACTTTCTC * MD:Z:9G12 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|0|22M|9G12 +49-1_1 0 19 7626 1 12M3I11M * 0 0 AAAGCACCTCCATTTGAGCTTGAAGC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +54-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23|TTTCAAGCCAGGGGGCGTTTTTC +56-1_1 0 19 44377 1 22M * 0 0 CTACAAAGGTAAGCACTTTATC * HI:i:0 MD:Z:9G9C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC +57-1_1 0 19 7626 255 23M * 0 0 AAAGCACCTCCAGAGCTTGAAGC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-3p|0|0|23M|23|AAAGCACCTCCAGAGCTTGAAGC +58-1_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCACTTTGGAGT * MD:Z:11C9 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|0|21M|11C9|GAAGGCGCTTCACTTTGGAGT +59-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|0|22M|22|CTACAAAGGGAAGCACTTTCTC +66-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGTGCATTTTCT * MD:Z:12G9 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|0|22M|12G9|TCAAAACTGAGGTGCATTTTCT +71-1_1 0 19 7626 255 23M * 0 0 AAAGCACCACCAGAGCTTGAAGC * MD:Z:8T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC +72-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGTAAGCACTTTCTC * MD:Z:9G12 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 90-1_1 0 19 44415 255 20M * 0 0 AAGGCGCTTCCCTTTGGAGT * MD:Z:20 NH:i:1 NM:i:0 YW:Z: 92-1_1 0 19 5338 1 9M1D3M1D7M * 0 0 TCAAAACTGGGGCATTTTC * HI:i:0 MD:Z:9^A3^G7 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: 94-1_1 0 19 44377 255 19M * 0 0 CTACAAAGGGAAGCACTTT * MD:Z:19 NH:i:1 NM:i:0 YW:Z: diff --git a/scripts/tests/files/mirna_tag_extension.sam b/scripts/tests/files/mirna_tag_extension.sam index 92d26a4..3979435 100644 --- a/scripts/tests/files/mirna_tag_extension.sam +++ b/scripts/tests/files/mirna_tag_extension.sam @@ -3,33 +3,33 @@ @PG ID:samtools PN:samtools VN:1.16.1 CL:samtools sort -n -o results/test_lib/header_sorted_catMappings.sam results/test_lib/concatenated_header_catMappings.sam @PG ID:samtools.1 PN:samtools PP:samtools VN:1.16.1 CL:samtools view -H results/test_lib/removeMultimappers.sam @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:samtools view -H results/test_lib/premir_intersectedAlignments.sam -8-2_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-3p|0|0|21M|21 -13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 -14-1_1 0 19 7590 1 20M3I3M * 0 0 TTTCAAGCCAGGGGGCGTTTCCGTTC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|0|20M3I3M|23 -15-1_1 0 19 7590 255 23M * 0 0 TTTCAAGTCAGGGGGCGTTTTTC * MD:Z:7C15 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|23M|7C15 -20-1_1 0 19 7590 255 15M1D7M * 0 0 TTTCAAGCCAGGGGGGTTTTTC * MD:Z:15^C7 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|15M1D7M|15^C7 -22-1_1 0 19 5338 1 18M3I4M * 0 0 TCAAAACTGAGGGGCATTGGATTCT * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|0|18M3I4M|22 -24-1_1 0 19 44414 255 11M1I10M * 0 0 GAAGGCGCTTCACCTTTGGAGT * MD:Z:22 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|0|11M1I10M|22 -26-1_1 0 19 7626 255 7M1I16M * 0 0 AAAGCACTCTCCAGAGCTTGAAGC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|7M1I16M|24 -31-1_1 0 19 7626 255 8M1D14M * 0 0 AAAGCACCCCAGAGCTTGAAGC * MD:Z:8^T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|8M1D14M|8^T14 -32-1_1 0 19 7626 1 23M * 0 0 AAAGCACCTCTTGAGCTTGAAGC * HI:i:0 MD:Z:10C0A11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|0|23M|10C0A11 -33-1_1 0 19 44377 255 18M1I4M * 0 0 CTACAAAGGGAAGCACTTGTCTC * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|0|18M1I4M|23 -34-1_1 0 19 7590 1 23M * 0 0 TTTCAAGCCAGATGGCGTTTTTC * HI:i:0 MD:Z:11G0G10 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|0|23M|11G0G10 -39-1_1 0 19 7590 255 19M1I4M * 0 0 TTTCAAGCCAGGGGGCGTTATTTC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|19M1I4M|24 -41-1_1 0 19 5338 255 15M1I7M * 0 0 TCAAAACTGAGGGGCTATTTTCT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|0|15M1I7M|23 -44-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22 -46-1_1 0 19 5338 1 22M * 0 0 TCAAAACTGAGGGGCATGCTCT * HI:i:0 MD:Z:17T0T3 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|0|22M|17T0T3 -48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21 -49-1_1 0 19 7626 1 12M3I11M * 0 0 AAAGCACCTCCATTTGAGCTTGAAGC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|0|12M3I11M|23 -54-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23 -56-1_1 0 19 44377 1 22M * 0 0 CTACAAAGGTAAGCACTTTATC * HI:i:0 MD:Z:9G9C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|22M|9G9C2 -57-1_1 0 19 7626 255 23M * 0 0 AAAGCACCTCCAGAGCTTGAAGC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-3p|0|0|23M|23 -58-1_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCACTTTGGAGT * MD:Z:11C9 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|0|21M|11C9 -59-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|0|22M|22 -66-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGTGCATTTTCT * MD:Z:12G9 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|0|22M|12G9 -71-1_1 0 19 7626 255 23M * 0 0 AAAGCACCACCAGAGCTTGAAGC * MD:Z:8T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|23M|8T14 -72-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGTAAGCACTTTCTC * MD:Z:9G12 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|0|22M|9G12 -90-1_1 0 19 44415 255 20M * 0 0 AAGGCGCTTCCCTTTGGAGT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-3p|1|0|20M|20 -92-1_1 0 19 5338 1 9M1D3M1D7M * 0 0 TCAAAACTGGGGCATTTTC * HI:i:0 MD:Z:9^A3^G7 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|-1|9M1D3M1D7M|9^A3^G7 -94-1_1 0 19 44377 255 19M * 0 0 CTACAAAGGGAAGCACTTT * MD:Z:19 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-3|19M|19 -95-1_1 0 19 44415 1 7M2D11M * 0 0 AAGGCGCCCCTTTGGAGT * HI:i:0 MD:Z:7^TT11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-3p|1|0|7M2D11M|7^TT11 +8-2_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-3p|0|0|21M|21|GAAGGCGCTTCCCTTTGGAGT +13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|3|11M3I11M|22|CTACAAAGGGAGGTAGCACTTTCTC +14-1_1 0 19 7590 1 20M3I3M * 0 0 TTTCAAGCCAGGGGGCGTTTCCGTTC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|3|20M3I3M|23|TTTCAAGCCAGGGGGCGTTTCCGTTC +15-1_1 0 19 7590 255 23M * 0 0 TTTCAAGTCAGGGGGCGTTTTTC * MD:Z:7C15 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|0|23M|7C15|TTTCAAGTCAGGGGGCGTTTTTC +20-1_1 0 19 7590 255 15M1D7M * 0 0 TTTCAAGCCAGGGGGGTTTTTC * MD:Z:15^C7 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|-1|15M1D7M|15^C7|TTTCAAGCCAGGGGGGTTTTTC +22-1_1 0 19 5338 1 18M3I4M * 0 0 TCAAAACTGAGGGGCATTGGATTCT * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|3|18M3I4M|22|TCAAAACTGAGGGGCATTGGATTCT +24-1_1 0 19 44414 255 11M1I10M * 0 0 GAAGGCGCTTCACCTTTGGAGT * MD:Z:22 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|1|11M1I10M|22|GAAGGCGCTTCACCTTTGGAGT +26-1_1 0 19 7626 255 7M1I16M * 0 0 AAAGCACTCTCCAGAGCTTGAAGC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|1|7M1I16M|24|AAAGCACTCTCCAGAGCTTGAAGC +31-1_1 0 19 7626 255 8M1D14M * 0 0 AAAGCACCCCAGAGCTTGAAGC * MD:Z:8^T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|-1|8M1D14M|8^T14|AAAGCACCCCAGAGCTTGAAGC +32-1_1 0 19 7626 1 23M * 0 0 AAAGCACCTCTTGAGCTTGAAGC * HI:i:0 MD:Z:10C0A11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|0|23M|10C0A11|AAAGCACCTCTTGAGCTTGAAGC +33-1_1 0 19 44377 255 18M1I4M * 0 0 CTACAAAGGGAAGCACTTGTCTC * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|1|18M1I4M|23|CTACAAAGGGAAGCACTTGTCTC +34-1_1 0 19 7590 1 23M * 0 0 TTTCAAGCCAGATGGCGTTTTTC * HI:i:0 MD:Z:11G0G10 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-5p|0|0|23M|11G0G10|TTTCAAGCCAGATGGCGTTTTTC +39-1_1 0 19 7590 255 19M1I4M * 0 0 TTTCAAGCCAGGGGGCGTTATTTC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-5p|0|1|19M1I4M|24|TTTCAAGCCAGGGGGCGTTATTTC +41-1_1 0 19 5338 255 15M1I7M * 0 0 TCAAAACTGAGGGGCTATTTTCT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|1|15M1I7M|23|TCAAAACTGAGGGGCTATTTTCT +44-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22|TCAAAACTGAGGGGCATTTTCT +46-1_1 0 19 5338 1 22M * 0 0 TCAAAACTGAGGGGCATGCTCT * HI:i:0 MD:Z:17T0T3 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|0|22M|17T0T3|TCAAAACTGAGGGGCATGCTCT +48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC +49-1_1 0 19 7626 1 12M3I11M * 0 0 AAAGCACCTCCATTTGAGCTTGAAGC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-498-3p|0|3|12M3I11M|23|AAAGCACCTCCATTTGAGCTTGAAGC +54-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23|TTTCAAGCCAGGGGGCGTTTTTC +56-1_1 0 19 44377 1 22M * 0 0 CTACAAAGGTAAGCACTTTATC * HI:i:0 MD:Z:9G9C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC +57-1_1 0 19 7626 255 23M * 0 0 AAAGCACCTCCAGAGCTTGAAGC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-3p|0|0|23M|23|AAAGCACCTCCAGAGCTTGAAGC +58-1_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCACTTTGGAGT * MD:Z:11C9 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-3p|0|0|21M|11C9|GAAGGCGCTTCACTTTGGAGT +59-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|0|22M|22|CTACAAAGGGAAGCACTTTCTC +66-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGTGCATTTTCT * MD:Z:12G9 NH:i:1 NM:i:1 YW:Z:hsa-miR-1323|0|0|22M|12G9|TCAAAACTGAGGTGCATTTTCT +71-1_1 0 19 7626 255 23M * 0 0 AAAGCACCACCAGAGCTTGAAGC * MD:Z:8T14 NH:i:1 NM:i:1 YW:Z:hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC +72-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGTAAGCACTTTCTC * MD:Z:9G12 NH:i:1 NM:i:1 YW:Z:hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC +90-1_1 0 19 44415 255 20M * 0 0 AAGGCGCTTCCCTTTGGAGT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-3p|1|0|20M|20|AAGGCGCTTCCCTTTGGAGT +92-1_1 0 19 5338 1 9M1D3M1D7M * 0 0 TCAAAACTGGGGCATTTTC * HI:i:0 MD:Z:9^A3^G7 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-1323|0|-3|9M1D3M1D7M|9^A3^G7|TCAAAACTGGGGCATTTTC +94-1_1 0 19 44377 255 19M * 0 0 CTACAAAGGGAAGCACTTT * MD:Z:19 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-3|19M|19|CTACAAAGGGAAGCACTTT +95-1_1 0 19 44415 1 7M2D11M * 0 0 AAGGCGCCCCTTTGGAGT * HI:i:0 MD:Z:7^TT11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-524-3p|1|-2|7M2D11M|7^TT11|AAGGCGCCCCTTTGGAGT diff --git a/scripts/tests/files/mirna_tag_id.sam b/scripts/tests/files/mirna_tag_id.sam index d45e954..7b47e3a 100644 --- a/scripts/tests/files/mirna_tag_id.sam +++ b/scripts/tests/files/mirna_tag_id.sam @@ -3,32 +3,32 @@ @PG ID:samtools PN:samtools VN:1.16.1 CL:samtools sort -n -o results/test_lib/header_sorted_catMappings.sam results/test_lib/concatenated_header_catMappings.sam @PG ID:samtools.1 PN:samtools PP:samtools VN:1.16.1 CL:samtools view -H results/test_lib/removeMultimappers.sam @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:samtools view -H results/test_lib/premir_intersectedAlignments.sam -8-2_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:MIMAT0002850|0|0|21M|21 -13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002849|0|0|11M3I11M|22 -14-1_1 0 19 7590 1 20M3I3M * 0 0 TTTCAAGCCAGGGGGCGTTTCCGTTC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002824|0|0|20M3I3M|23 -15-1_1 0 19 7590 255 23M * 0 0 TTTCAAGTCAGGGGGCGTTTTTC * MD:Z:7C15 NH:i:1 NM:i:1 YW:Z:MIMAT0002824|0|0|23M|7C15 -20-1_1 0 19 7590 255 15M1D7M * 0 0 TTTCAAGCCAGGGGGGTTTTTC * MD:Z:15^C7 NH:i:1 NM:i:1 YW:Z:MIMAT0002824|0|0|15M1D7M|15^C7 -22-1_1 0 19 5338 1 18M3I4M * 0 0 TCAAAACTGAGGGGCATTGGATTCT * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0005795|0|0|18M3I4M|22 -24-1_1 0 19 44414 255 11M1I10M * 0 0 GAAGGCGCTTCACCTTTGGAGT * MD:Z:22 NH:i:1 NM:i:1 YW:Z:MIMAT0002850|0|0|11M1I10M|22 -26-1_1 0 19 7626 255 7M1I16M * 0 0 AAAGCACTCTCCAGAGCTTGAAGC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:MIMAT0037323|0|0|7M1I16M|24 -31-1_1 0 19 7626 255 8M1D14M * 0 0 AAAGCACCCCAGAGCTTGAAGC * MD:Z:8^T14 NH:i:1 NM:i:1 YW:Z:MIMAT0037323|0|0|8M1D14M|8^T14 -32-1_1 0 19 7626 1 23M * 0 0 AAAGCACCTCTTGAGCTTGAAGC * HI:i:0 MD:Z:10C0A11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0037323|0|0|23M|10C0A11 -33-1_1 0 19 44377 255 18M1I4M * 0 0 CTACAAAGGGAAGCACTTGTCTC * MD:Z:23 NH:i:1 NM:i:1 YW:Z:MIMAT0002849|0|0|18M1I4M|23 -34-1_1 0 19 7590 1 23M * 0 0 TTTCAAGCCAGATGGCGTTTTTC * HI:i:0 MD:Z:11G0G10 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002824|0|0|23M|11G0G10 -39-1_1 0 19 7590 255 19M1I4M * 0 0 TTTCAAGCCAGGGGGCGTTATTTC * MD:Z:24 NH:i:1 NM:i:1 YW:Z:MIMAT0002824|0|0|19M1I4M|24 -41-1_1 0 19 5338 255 15M1I7M * 0 0 TCAAAACTGAGGGGCTATTTTCT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:MIMAT0005795|0|0|15M1I7M|23 -44-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:MIMAT0005795|0|0|22M|22 -46-1_1 0 19 5338 1 22M * 0 0 TCAAAACTGAGGGGCATGCTCT * HI:i:0 MD:Z:17T0T3 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0005795|0|0|22M|17T0T3 +8-2_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:MIMAT0002850|0|0|21M|21|GAAGGCGCTTCCCTTTGGAGT +13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +14-1_1 0 19 7590 1 20M3I3M * 0 0 TTTCAAGCCAGGGGGCGTTTCCGTTC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +15-1_1 0 19 7590 255 23M * 0 0 TTTCAAGTCAGGGGGCGTTTTTC * MD:Z:7C15 NH:i:1 NM:i:1 YW:Z:MIMAT0002824|0|0|23M|7C15|TTTCAAGTCAGGGGGCGTTTTTC +20-1_1 0 19 7590 255 15M1D7M * 0 0 TTTCAAGCCAGGGGGGTTTTTC * MD:Z:15^C7 NH:i:1 NM:i:1 YW:Z: +22-1_1 0 19 5338 1 18M3I4M * 0 0 TCAAAACTGAGGGGCATTGGATTCT * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +24-1_1 0 19 44414 255 11M1I10M * 0 0 GAAGGCGCTTCACCTTTGGAGT * MD:Z:22 NH:i:1 NM:i:1 YW:Z: +26-1_1 0 19 7626 255 7M1I16M * 0 0 AAAGCACTCTCCAGAGCTTGAAGC * MD:Z:24 NH:i:1 NM:i:1 YW:Z: +31-1_1 0 19 7626 255 8M1D14M * 0 0 AAAGCACCCCAGAGCTTGAAGC * MD:Z:8^T14 NH:i:1 NM:i:1 YW:Z: +32-1_1 0 19 7626 1 23M * 0 0 AAAGCACCTCTTGAGCTTGAAGC * HI:i:0 MD:Z:10C0A11 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0037323|0|0|23M|10C0A11|AAAGCACCTCTTGAGCTTGAAGC +33-1_1 0 19 44377 255 18M1I4M * 0 0 CTACAAAGGGAAGCACTTGTCTC * MD:Z:23 NH:i:1 NM:i:1 YW:Z: +34-1_1 0 19 7590 1 23M * 0 0 TTTCAAGCCAGATGGCGTTTTTC * HI:i:0 MD:Z:11G0G10 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002824|0|0|23M|11G0G10|TTTCAAGCCAGATGGCGTTTTTC +39-1_1 0 19 7590 255 19M1I4M * 0 0 TTTCAAGCCAGGGGGCGTTATTTC * MD:Z:24 NH:i:1 NM:i:1 YW:Z: +41-1_1 0 19 5338 255 15M1I7M * 0 0 TCAAAACTGAGGGGCTATTTTCT * MD:Z:23 NH:i:1 NM:i:1 YW:Z: +44-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:MIMAT0005795|0|0|22M|22|TCAAAACTGAGGGGCATTTTCT +46-1_1 0 19 5338 1 22M * 0 0 TCAAAACTGAGGGGCATGCTCT * HI:i:0 MD:Z:17T0T3 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0005795|0|0|22M|17T0T3|TCAAAACTGAGGGGCATGCTCT 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z: -49-1_1 0 19 7626 1 12M3I11M * 0 0 AAAGCACCTCCATTTGAGCTTGAAGC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0037323|0|0|12M3I11M|23 -54-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:MIMAT0002824|0|0|23M|23 -56-1_1 0 19 44377 1 22M * 0 0 CTACAAAGGTAAGCACTTTATC * HI:i:0 MD:Z:9G9C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002849|0|0|22M|9G9C2 -57-1_1 0 19 7626 255 23M * 0 0 AAAGCACCTCCAGAGCTTGAAGC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:MIMAT0037323|0|0|23M|23 -58-1_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCACTTTGGAGT * MD:Z:11C9 NH:i:1 NM:i:1 YW:Z:MIMAT0002850|0|0|21M|11C9 -59-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:MIMAT0002849|0|0|22M|22 -66-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGTGCATTTTCT * MD:Z:12G9 NH:i:1 NM:i:1 YW:Z:MIMAT0005795|0|0|22M|12G9 -71-1_1 0 19 7626 255 23M * 0 0 AAAGCACCACCAGAGCTTGAAGC * MD:Z:8T14 NH:i:1 NM:i:1 YW:Z:MIMAT0037323|0|0|23M|8T14 -72-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGTAAGCACTTTCTC * MD:Z:9G12 NH:i:1 NM:i:1 YW:Z:MIMAT0002849|0|0|22M|9G12 +49-1_1 0 19 7626 1 12M3I11M * 0 0 AAAGCACCTCCATTTGAGCTTGAAGC * HI:i:0 MD:Z:23 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: +54-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:MIMAT0002824|0|0|23M|23|TTTCAAGCCAGGGGGCGTTTTTC +56-1_1 0 19 44377 1 22M * 0 0 CTACAAAGGTAAGCACTTTATC * HI:i:0 MD:Z:9G9C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002849|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC +57-1_1 0 19 7626 255 23M * 0 0 AAAGCACCTCCAGAGCTTGAAGC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:MIMAT0037323|0|0|23M|23|AAAGCACCTCCAGAGCTTGAAGC +58-1_1 0 19 44414 255 21M * 0 0 GAAGGCGCTTCACTTTGGAGT * MD:Z:11C9 NH:i:1 NM:i:1 YW:Z:MIMAT0002850|0|0|21M|11C9|GAAGGCGCTTCACTTTGGAGT +59-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:MIMAT0002849|0|0|22M|22|CTACAAAGGGAAGCACTTTCTC +66-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGTGCATTTTCT * MD:Z:12G9 NH:i:1 NM:i:1 YW:Z:MIMAT0005795|0|0|22M|12G9|TCAAAACTGAGGTGCATTTTCT +71-1_1 0 19 7626 255 23M * 0 0 AAAGCACCACCAGAGCTTGAAGC * MD:Z:8T14 NH:i:1 NM:i:1 YW:Z:MIMAT0037323|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC +72-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGTAAGCACTTTCTC * MD:Z:9G12 NH:i:1 NM:i:1 YW:Z:MIMAT0002849|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 90-1_1 0 19 44415 255 20M * 0 0 AAGGCGCTTCCCTTTGGAGT * MD:Z:20 NH:i:1 NM:i:0 YW:Z: 92-1_1 0 19 5338 1 9M1D3M1D7M * 0 0 TCAAAACTGGGGCATTTTC * HI:i:0 MD:Z:9^A3^G7 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: 94-1_1 0 19 44377 255 19M * 0 0 CTACAAAGGGAAGCACTTT * MD:Z:19 NH:i:1 NM:i:0 YW:Z: From dc79f3636a353afb269c7ceb42541d3be8c80429 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 19:35:50 +0200 Subject: [PATCH 22/42] test: update unit tests --- scripts/tests/test_iso_name_tagging.py | 250 ++++++++++++++++++++++++- 1 file changed, 249 insertions(+), 1 deletion(-) diff --git a/scripts/tests/test_iso_name_tagging.py b/scripts/tests/test_iso_name_tagging.py index ef1881c..fe4c1a6 100644 --- a/scripts/tests/test_iso_name_tagging.py +++ b/scripts/tests/test_iso_name_tagging.py @@ -4,9 +4,16 @@ from pathlib import Path import sys +import pysam import pytest -from ..iso_name_tagging import main, parse_arguments +from ..iso_name_tagging import ( + attributes_dictionary, + get_tags, + main, + parse_arguments, + parse_intersect_output, +) @pytest.fixture @@ -48,6 +55,247 @@ def bed_sam_id(): return bed_file, sam_file, output_file +# pylint: disable=line-too-long +@pytest.fixture +def attributes_gtf_gff(): + """Attributes strings in GFF3 and GTF format.""" + gff_attributes = "ID=MIMAT0019022;Alias=MIMAT0019022;Name=hsa-miR-4488;Derives_from=MI0016849" # noqa: E501 + gtf_attributes = 'ID "MIMAT0019022";Alias "MIMAT0019022";Name "hsa-miR-4488";Derives_from "MI0016849"' # noqa: E501 + dict_attributes = { + "id": "MIMAT0019022", + "alias": "MIMAT0019022", + "name": "hsa-miR-4488", + "derives_from": "MI0016849", + } + + return gff_attributes, gtf_attributes, dict_attributes + + +# pylint: enable=line-too-long + + +@pytest.fixture +def alns(): + """Create sample AlignedSegment objects.""" + aln1 = pysam.AlignedSegment() + aln1.cigarstring = "21M" + aln1.query_name = "8-2_1" + aln1.query_sequence = "GAAGGCGCTTCCCTTTGGAGT" + aln1.reference_id = 19 + aln1.reference_start = 44414 + aln1.set_tag("MD", 21) + aln1.set_tag("NH", 2) + aln1.set_tag("HI", 1) + + # Alignment with 3 insertions + aln2 = pysam.AlignedSegment() + aln2.cigarstring = "21M" + aln2.query_name = "8-2_1" + aln2.query_sequence = "GAAGGCGCTTCCCTTTGGAGT" + aln2.reference_id = 19 + aln2.reference_start = 44409 + aln2.set_tag("MD", 21) + aln2.set_tag("NH", 2) + aln2.set_tag("HI", 1) + + return aln1, aln2 + + +@pytest.fixture +def intersect_dicts(): + """Dictionaries of the intersect output BED files.""" + inter_name = { + "22-1_1": [("hsa-miR-1323", 5338, 5359)], + "41-1_1": [("hsa-miR-1323", 5338, 5359)], + "44-1_1": [("hsa-miR-1323", 5338, 5359)], + "46-1_1": [("hsa-miR-1323", 5338, 5359)], + "48-1_1": [("hsa-miR-1323", 5338, 5359)], + "66-1_1": [("hsa-miR-1323", 5338, 5359)], + "92-1_1": [("hsa-miR-1323", 5338, 5359)], + "14-1_1": [("hsa-miR-498-5p", 7590, 7612)], + "15-1_1": [("hsa-miR-498-5p", 7590, 7612)], + "20-1_1": [("hsa-miR-498-5p", 7590, 7612)], + "34-1_1": [("hsa-miR-498-5p", 7590, 7612)], + "39-1_1": [("hsa-miR-498-5p", 7590, 7612)], + "54-1_1": [("hsa-miR-498-5p", 7590, 7612)], + "26-1_1": [("hsa-miR-498-3p", 7626, 7648)], + "31-1_1": [("hsa-miR-498-3p", 7626, 7648)], + "32-1_1": [("hsa-miR-498-3p", 7626, 7648)], + "49-1_1": [("hsa-miR-498-3p", 7626, 7648)], + "57-1_1": [("hsa-miR-498-3p", 7626, 7648)], + "71-1_1": [("hsa-miR-498-3p", 7626, 7648)], + "13-1_1": [("hsa-miR-524-5p", 44377, 44398)], + "33-1_1": [("hsa-miR-524-5p", 44377, 44398)], + "56-1_1": [("hsa-miR-524-5p", 44377, 44398)], + "59-1_1": [("hsa-miR-524-5p", 44377, 44398)], + "72-1_1": [("hsa-miR-524-5p", 44377, 44398)], + "94-1_1": [("hsa-miR-524-5p", 44377, 44398)], + "8-2_1": [("hsa-miR-524-3p", 44414, 44434)], + "24-1_1": [("hsa-miR-524-3p", 44414, 44434)], + "58-1_1": [("hsa-miR-524-3p", 44414, 44434)], + "90-1_1": [("hsa-miR-524-3p", 44414, 44434)], + "95-1_1": [("hsa-miR-524-3p", 44414, 44434)], + } + inter_id_alias = { + "22-1_1": [("MIMAT0005795", 5338, 5359)], + "41-1_1": [("MIMAT0005795", 5338, 5359)], + "44-1_1": [("MIMAT0005795", 5338, 5359)], + "46-1_1": [("MIMAT0005795", 5338, 5359)], + "48-1_1": [("MIMAT0005795", 5338, 5359)], + "66-1_1": [("MIMAT0005795", 5338, 5359)], + "92-1_1": [("MIMAT0005795", 5338, 5359)], + "14-1_1": [("MIMAT0002824", 7590, 7612)], + "15-1_1": [("MIMAT0002824", 7590, 7612)], + "20-1_1": [("MIMAT0002824", 7590, 7612)], + "34-1_1": [("MIMAT0002824", 7590, 7612)], + "39-1_1": [("MIMAT0002824", 7590, 7612)], + "54-1_1": [("MIMAT0002824", 7590, 7612)], + "26-1_1": [("MIMAT0037323", 7626, 7648)], + "31-1_1": [("MIMAT0037323", 7626, 7648)], + "32-1_1": [("MIMAT0037323", 7626, 7648)], + "49-1_1": [("MIMAT0037323", 7626, 7648)], + "57-1_1": [("MIMAT0037323", 7626, 7648)], + "71-1_1": [("MIMAT0037323", 7626, 7648)], + "13-1_1": [("MIMAT0002849", 44377, 44398)], + "33-1_1": [("MIMAT0002849", 44377, 44398)], + "56-1_1": [("MIMAT0002849", 44377, 44398)], + "59-1_1": [("MIMAT0002849", 44377, 44398)], + "72-1_1": [("MIMAT0002849", 44377, 44398)], + "94-1_1": [("MIMAT0002849", 44377, 44398)], + "8-2_1": [("MIMAT0002850", 44414, 44434)], + "24-1_1": [("MIMAT0002850", 44414, 44434)], + "58-1_1": [("MIMAT0002850", 44414, 44434)], + "90-1_1": [("MIMAT0002850", 44414, 44434)], + "95-1_1": [("MIMAT0002850", 44414, 44434)], + } + inter_extension = { + "22-1_1": [("hsa-miR-1323", 5341, 5356)], + "41-1_1": [("hsa-miR-1323", 5341, 5356)], + "44-1_1": [("hsa-miR-1323", 5341, 5356)], + "46-1_1": [("hsa-miR-1323", 5341, 5356)], + "48-1_1": [("hsa-miR-1323", 5341, 5356)], + "66-1_1": [("hsa-miR-1323", 5341, 5356)], + "92-1_1": [("hsa-miR-1323", 5341, 5356)], + "14-1_1": [("hsa-miR-498-5p", 7593, 7609)], + "15-1_1": [("hsa-miR-498-5p", 7593, 7609)], + "20-1_1": [("hsa-miR-498-5p", 7593, 7609)], + "34-1_1": [("hsa-miR-498-5p", 7593, 7609)], + "39-1_1": [("hsa-miR-498-5p", 7593, 7609)], + "54-1_1": [("hsa-miR-498-5p", 7593, 7609)], + "26-1_1": [("hsa-miR-498-3p", 7629, 7645)], + "31-1_1": [("hsa-miR-498-3p", 7629, 7645)], + "32-1_1": [("hsa-miR-498-3p", 7629, 7645)], + "49-1_1": [("hsa-miR-498-3p", 7629, 7645)], + "57-1_1": [("hsa-miR-498-3p", 7629, 7645)], + "71-1_1": [("hsa-miR-498-3p", 7629, 7645)], + "13-1_1": [("hsa-miR-524-5p", 44380, 44395)], + "33-1_1": [("hsa-miR-524-5p", 44380, 44395)], + "56-1_1": [("hsa-miR-524-5p", 44380, 44395)], + "59-1_1": [("hsa-miR-524-5p", 44380, 44395)], + "72-1_1": [("hsa-miR-524-5p", 44380, 44395)], + "94-1_1": [("hsa-miR-524-5p", 44380, 44395)], + "8-2_1": [("hsa-miR-524-3p", 44417, 44431)], + "24-1_1": [("hsa-miR-524-3p", 44417, 44431)], + "58-1_1": [("hsa-miR-524-3p", 44417, 44431)], + "90-1_1": [("hsa-miR-524-3p", 44417, 44431)], + "95-1_1": [("hsa-miR-524-3p", 44417, 44431)], + } + + return inter_name, inter_id_alias, inter_extension + + +class TestAttributesDictionary: + """Test 'attributes_dictionary()' function.""" + + def test_attributes_dictionary_gff(self, attributes_gtf_gff): + """Test get attributes dictionary from GFF3 attributes string.""" + gff_attr, gtf_attr, dict_attr = attributes_gtf_gff + + assert dict_attr == attributes_dictionary(gff_attr) + + def test_attributes_dictionary_gtf(self, attributes_gtf_gff): + """Test get attributes dictionary from GTF attributes string.""" + gff_attr, gtf_attr, dict_attr = attributes_gtf_gff + + assert dict_attr == attributes_dictionary(gtf_attr) + + +class TestParseIntersectOutput: + """Test 'parse_intersect_output()' function.""" + + def test_parse_intersect_output_empty_bed(self, empty_files): + """Test parse intersect empty output.""" + empty_bed, empty_sam = empty_files + + assert parse_intersect_output(intersect_file=empty_bed) is None + + def test_parse_intersect_output_name_id(self, bed_sam, intersect_dicts): + """Test parse intersect output using 'name' as ID.""" + in_bed, in_sam, out_f = bed_sam + out_name, out_id_alias, out_ext_3 = intersect_dicts + + out_inter = parse_intersect_output(intersect_file=in_bed) + + assert sorted(out_inter.items()) == sorted(out_name.items()) + + def test_parse_intersect_output_alias_id(self, bed_sam, intersect_dicts): + """Test parse intersect output using 'alias' as ID.""" + in_bed, in_sam, out_f = bed_sam + out_name, out_id_alias, out_ext_3 = intersect_dicts + + out_inter = parse_intersect_output(intersect_file=in_bed, id="alias") + + assert sorted(out_inter.items()) == sorted(out_id_alias.items()) + + def test_parse_intersect_output_id_id(self, bed_sam, intersect_dicts): + """Test parse intersect output using 'id' as ID.""" + in_bed, in_sam, out_f = bed_sam + out_name, out_id_alias, out_ext_3 = intersect_dicts + + out_inter = parse_intersect_output(intersect_file=in_bed, id="id") + + assert sorted(out_inter.items()) == sorted(out_id_alias.items()) + + def test_parse_intersect_output_extend_3(self, bed_sam, intersect_dicts): + """Test parse intersect output with an extension of 3 nucleotides.""" + in_bed, in_sam, out_f = bed_sam + out_name, out_id_alias, out_ext_3 = intersect_dicts + + out_inter = parse_intersect_output(intersect_file=in_bed, extension=3) + + assert sorted(out_inter.items()) == sorted(out_ext_3.items()) + + +class TestGetTags: + """Test 'get_tags()' function.""" + + def test_get_tags_within_shift_range_1_extn(self, alns, intersect_dicts): + """Test get tags within shift range +/-1.""" + aln_1, aln_2 = alns + out_name, out_id_alias, out_ext_3 = intersect_dicts + + tags = get_tags( + intersecting_mirna=out_name[aln_1.query_name], + alignment=aln_1, + extend=1, + ) + expected = "hsa-miR-524-3p|1|1|21M|21|GAAGGCGCTTCCCTTTGGAGT" + + assert next(iter(tags)) == expected + + def test_get_tags_out_shift_range(self, alns, intersect_dicts): + """Test get tags outside shift range +/-0.""" + aln_1, aln_2 = alns + out_name, out_id_alias, out_ext_3 = intersect_dicts + + tags = get_tags( + intersecting_mirna=out_name[aln_1.query_name], + alignment=aln_2, + extend=0, + ) + assert tags == set() + + class TestParseArguments: """Test 'parse_arguments()' function.""" From 1439b5eecc246d7d92bdea8efc2cdede45189d53 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 19:50:29 +0200 Subject: [PATCH 23/42] ci: update expected output --- test/expected_output.md5 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/expected_output.md5 b/test/expected_output.md5 index 1a2161a..ad81a5a 100644 --- a/test/expected_output.md5 +++ b/test/expected_output.md5 @@ -1,10 +1,10 @@ -68f943f89b52d628851dd97fb1399d68 results/TABLES/all_mirna_counts.tab +2f1b225c294ca0e22f565b4533b9c362 results/TABLES/all_mirna_counts.tab 363ecee318c57ee7e2e45ca468007baa results/TABLES/all_pri-mir_counts.tab a0d36054628fbe1975e142d638fbb0ff results/test_lib/alignments_intersecting_mirna_uncollapsed_sorted.bam.bai 1371823fdc7a218e1e92ad546cfac585 results/test_lib/alignments_intersecting_mirna_uncollapsed_sorted.bam cc01c7884838a597c587437cb0acf64e results/test_lib/alignments_intersecting_mirna.sam b1eb81426f890d671bba8c8a815edc1e results/test_lib/alignments_intersecting_primir.sam -eec9be6cda61d2728290c92c1209f455 results/intermediates/TABLES/mirna_counts_test_lib +48bc2337cce6f361d8a2a2c4b09b6011 results/intermediates/TABLES/mirna_counts_test_lib a844e3a29159e36e2f17a0646d1e8c5f results/intermediates/TABLES/pri-mir_counts_test_lib 48e605df55bf2dd37ea5a5a74eb5872a results/intermediates/test_lib/mappings_all.sam e9aac4afeb2053385d60f5e4b07a9774 results/intermediates/test_lib/mappings_all_removed_inferiors.sam @@ -15,7 +15,7 @@ e632f8984d423d46bbb377ec75468521 results/intermediates/test_lib/transcriptome_m a124a5afdb5f7bfbcc5683260556c9c4 results/intermediates/test_lib/mappings_all_no_header.sam d62630102c33d43d593af14c2a642839 results/intermediates/test_lib/alignments_all.sam defdc8c46e1d73692edde0e0278f2d5e results/intermediates/test_lib/oligomap_genome_mappings.oligomap -81103749d61bc55ee2cfc84ca1527456 results/intermediates/test_lib/alignments_intersecting_mirna_tag.sam +577d3675ef2bc42f80c7c2ea2f9e5004 results/intermediates/test_lib/alignments_intersecting_mirna_tag.sam 76643f87bb2e2bff77d1b1223d7720b5 results/intermediates/test_lib/segemehl_genome_mappings.sam d41d8cd98f00b204e9800998ecf8427e results/intermediates/test_lib/transcriptome_mappings_to_genome.sam d41d8cd98f00b204e9800998ecf8427e results/intermediates/test_lib/oligomap_transcriptome_mappings.oligomap @@ -32,7 +32,7 @@ f5cb65466d328036a15b66cfbd4d8419 results/intermediates/test_lib/oligomap_genome 6cbdb9299e09b3e39b79a50db69226b5 results/intermediates/test_lib/transcriptome_mappings_no_header.sam e632f8984d423d46bbb377ec75468521 results/intermediates/test_lib/transcriptome_mappings.sam 947607be69c16246f8dc9adbd9b971c8 results/intermediates/test_lib/oligomap_genome_mappings.sam -ce3fcd037e0a6a0b1a7a3253219e7053 results/intermediates/test_lib/alignments_intersecting_mirna_sorted_tag.sam +2b65293cb0dea3fc73ce4ae816047e3a results/intermediates/test_lib/alignments_intersecting_mirna_sorted_tag.sam 53764354c520d9700f13761c2721d8aa results/intermediates/test_lib/alignments_intersecting_primir_sorted.bam d41d8cd98f00b204e9800998ecf8427e results/intermediates/test_lib/oligomap_transcriptome_mappings.sam a124a5afdb5f7bfbcc5683260556c9c4 results/intermediates/test_lib/genome_mappings_no_header.sam From ad7afe9ad2b37e31b0d2389038ad546fe7b3d085 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 19:50:47 +0200 Subject: [PATCH 24/42] docs: update isomiR name format --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 68a49f6..4c6c24d 100644 --- a/README.md +++ b/README.md @@ -420,7 +420,7 @@ InDel or a mismatch on its sequence when compared to the canonical miRNA it maps and intersects with. _MIRFLOWZ_ employs an unambiguous notation to classify isomiRs using the -format `miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and +format `miRNA_name|5p-shift|3p-shift|CIGAR|MD|read_seq`, where `5p-shift` and `3p-shift` represent the differences between the annotated mature miRNA start and end positions and those of the read alignment, respectively. From 1d8c54126a36b39cb33bddfd85772284f0476847 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 17 Aug 2024 19:50:55 +0200 Subject: [PATCH 25/42] docs: update isomiR name format --- pipeline_documentation.md | 74 +++++++++++++++++++-------------------- 1 file changed, 37 insertions(+), 37 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index 7e1c6c2..6332027 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -1235,9 +1235,9 @@ with a [**custom script**][custom-script-iso-tag]. > extended ones. Each alignment gets an extra tag (`YW:Z`) with either the > (iso)miR(s) it is considered to really intersect with or an empty string > otherwise. The format of the intersecting mature miRNA species is -> `miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and `3p-shift` are -> the difference between the miRNA start and end coordinates and the -> alignment's ones respectively. +> `miRNA_name|5p-shift|3p-shift|CIGAR|MD|read_name`, where `5p-shift` and +> `3p-shift` are the difference between the miRNA start and end coordinates and +> the alignment's ones respectively. - **Input** - Alignments file, filtered (`.sam`); from @@ -1261,7 +1261,7 @@ IN miRNA annotations: IN SAM record: 1-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 NEW TAG: - YW:Z:hsa-miR-524-5p|0|0|22M|22 + YW:Z:hsa-miR-524-5p|0|0|22M|22|CTACAAAGGGAAGCACTTTCTC Example 2 | Intersecting an isomiR (no shifts) @@ -1271,7 +1271,7 @@ IN miRNA annotations: IN SAM record: 1-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 NEW TAG: - YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 + YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22|CTACAAAGGGAGGTAGCACTTTCTC Example 3 | Intersecting an isomiR (no InDels nor mismatches) @@ -1281,7 +1281,7 @@ IN miRNA annotations: IN SAM record: 1-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 NEW TAG: - YW:Z:hsa-miR-1323|0|-1|21M|21 + YW:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC Example 4 | Not intersecting an (iso)miR @@ -1355,20 +1355,20 @@ Data: Contribution: 4/2 = 2 miRNA species: - Tag name: hsa-miR-520b-3p|0|0|21M|21 + Tag name: hsa-miR-520b-3p|0|0|21M|21|AAAGTGCTTCCTTTTAGAGGG Type: Canonical Table name: hsa-miR-520b-3p Total count: 2 - Tag name: hsa-miR-520c-3p|0|-1|21M|21 + Tag name: hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG Type: isomiR - Table name: hsa-miR-520c-3p|0|-1|21M|21 + Table name: hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG Total count: 2 OUT table: - ID lib_name - hsa-miR-520b-3p 2 - hsa-miR-520c-3p|0|-1|21M|21 2 + ID lib_name + hsa-miR-520b-3p 2 + hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG 2 Example 2 | Different isomiRs @@ -1386,26 +1386,26 @@ Data: Contribution: 1/3 = 0.33 miRNA species: - Tag name: hsa-miR-526b-3p|1|-1|20M|20 + Tag name: hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Type: isomiR - Table name: hsa-miR-526b-3p|1|-1|20M|20 + Table name: hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Total count: 0.33 - Tag name: hsa-miR-520b-3p|0|-1|20M|20 + Tag name: hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Type: isomiR - Table name: hsa-miR-520b-3p|0|-1|20M|20 + Table name: hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Total count: 0.33 - Tag name: hsa-miR-520c-3p|0|-2|20M|20 + Tag name: hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG Type: isomiR - Table name: hsa-miR-520c-3p|0|-2|20M|20 + Table name: hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG Total count: 0.33 OUT table: - ID lib_name - hsa-miR-520b-3p|0|-1|20M|20 0.33 - hsa-miR-520c-3p|0|-2|20M|20 0.33 - hsa-miR-526b-3p|1|-1|20M|20 0.33 + ID lib_name + hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 + hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 + hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 ``` @@ -1506,27 +1506,27 @@ Merge all the tables from the different libraries into a single one with a ```console IN library 1 - ID lib_1 - hsa-miR-524-5p 1 - hsa-miR-524-5p|0|0|22M|9G12 1 - hsa-miR-524-5p|0|0|22M|9G9C2 1 + ID lib_1 + hsa-miR-524-5p 1 + hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 1 + hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC 1 IN library 2 - ID lib_2 - hsa-miR-524-5p 1 - hsa-miR-1283 1 - hsa-miR-1283|-1|-2|21M|21 1 + ID lib_2 + hsa-miR-524-5p 1 + hsa-miR-1283 1 + hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC 1 IN library 3 - ID lib_3 + ID lib_3 OUT table - ID lib_1 lib_2 lib_3 - hsa-miR-524-5p 1 1 NA - hsa-miR-524-5p|0|0|22M|9G12 1 NA NA - hsa-miR-524-5p|0|0|22M|9G9C2 1 NA NA - hsa-miR-1283 NA 1 NA - hsa-miR-1283|-1|-2|21M|21 NA 1 NA + ID lib_1 lib_2 lib_3 + hsa-miR-524-5p 1 1 NA + hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 1 NA NA + hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC 1 NA NA + hsa-miR-1283 NA 1 NA + hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC NA 1 NA ``` From 1edc99b3af74279b9af9bb52d714037accd4a3ee Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 13:44:50 +0200 Subject: [PATCH 26/42] test: adjust for new isomir name format --- scripts/tests/test_mirna_quantification.py | 29 ++++++++++++++++------ 1 file changed, 22 insertions(+), 7 deletions(-) diff --git a/scripts/tests/test_mirna_quantification.py b/scripts/tests/test_mirna_quantification.py index e08d630..162e7e0 100644 --- a/scripts/tests/test_mirna_quantification.py +++ b/scripts/tests/test_mirna_quantification.py @@ -95,7 +95,7 @@ def read_len_sam_file(): def uncollapsed_sam_file(): """Import path to uncollapsed test files.""" sam_file = Path("files/in_aln_tag.sam") - out_table = Path("files/uncollpased_iso_mirna_quantification") + out_table = Path("files/uncollapsed_iso_mirna_quantification") return sam_file, out_table @@ -176,7 +176,7 @@ def test_correct_input(self, monkeypatch, empty_file): sys, "argv", [ - "mirna__quantification", + "mirna_quantification", str(in_sam), "--lib", "test_lib", @@ -261,17 +261,32 @@ class TestGetName: def test_canonical(self): """Test canonical miRNA name.""" name = ["mirna", "hsa-miR-1323"] - assert get_name("hsa-miR-1323|0|0|22M|22") == name + assert ( + get_name("hsa-miR-1323|0|0|22M|22|TCAAAACTGAGGGGCATTGGATTCT") + == name + ) def test_iso_0_shift(self): """Test isoform with 0 shift.""" - name = ["isomir", "hsa-miR-1323|0|0|18M3I4M|22"] - assert get_name("hsa-miR-1323|0|0|18M3I4M|22") == name + name = [ + "isomir", + "hsa-miR-1323|0|0|18M3I4M|22|TCAAAACTGAGGGGCATTGGATTCT", + ] + assert ( + get_name("hsa-miR-1323|0|0|18M3I4M|22|TCAAAACTGAGGGGCATTGGATTCT") + == name + ) def test_iso(self): """Test isoform with shift.""" - name = ["isomir", "hsa-miR-1323|2|0|18M3I4M|22"] - assert get_name("hsa-miR-1323|2|0|18M3I4M|22") == name + name = [ + "isomir", + "hsa-miR-1323|2|0|18M3I4M|22|TCAAAACTGAGGGGCATTGGATTCT", + ] + assert ( + get_name("hsa-miR-1323|2|0|18M3I4M|22|TCAAAACTGAGGGGCATTGGATTCT") + == name + ) class TestMain: From 68fb65530a6f9a2af387e410180148d299f7b68e Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 13:45:26 +0200 Subject: [PATCH 27/42] test: adjust for isomir new name format --- scripts/tests/files/in_aln_tag.sam | 506 ++++++++--------- scripts/tests/files/in_aln_tag_XN.sam | 517 +++++++++--------- scripts/tests/files/in_aln_tag_missing_nh.sam | 510 ++++++++--------- scripts/tests/files/iso_mirna_quantification | 265 ++++----- scripts/tests/files/iso_quantification | 265 ++++----- .../files/len_ids_iso_mirna_quantification | 265 ++++----- .../tests/files/len_iso_mirna_quantification | 265 ++++----- .../files/missing_nh_iso_mirna_quantification | 281 +++++----- .../files/read_ids_iso_mirna_quantification | 265 ++++----- .../files/reads_ids_iso_mirna_quantification | 160 ++++++ .../uncollapsed_iso_mirna_quantification | 160 ++++++ ...lapsed_missing_nh_iso_mirna_quantification | 281 +++++----- .../files/xn_tag_iso_mirna_quantification | 265 ++++----- 13 files changed, 2179 insertions(+), 1826 deletions(-) create mode 100644 scripts/tests/files/reads_ids_iso_mirna_quantification create mode 100644 scripts/tests/files/uncollapsed_iso_mirna_quantification diff --git a/scripts/tests/files/in_aln_tag.sam b/scripts/tests/files/in_aln_tag.sam index cdac5ec..52072be 100644 --- a/scripts/tests/files/in_aln_tag.sam +++ b/scripts/tests/files/in_aln_tag.sam @@ -13,256 +13,256 @@ 445515-1_1 0 19 53506 1 9M1D7M * 0 0 AAGAAAGTGTTCTCTA * HI:i:0 MD:Z:9^C6T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: 138559-2_2 256 19 75885 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z: 641705-1_1 0 19 121288 1 9M1I6M * 0 0 TGGAAAGTGGCTGAGA * HI:i:0 MD:Z:12C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: -709268-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21 -528546-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22 -270342-1_1 0 19 121040 255 20M * 0 0 ACTCAAACTGTGGGGGCACT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-371a-5p|0|0|20M|20 -840419-1_1 0 19 121040 1 23M * 0 0 ACTCAAACTGTGGGGGCCCTTAG * HI:i:0 MD:Z:17A3T0C0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-371a-5p|0|3|23M|17A3T0C0 -120522-2_1 16 19 121038 255 22M * 0 0 GCACTCAAACTGTGGGGGCACT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-371b-3p|0|-1|22M|22 -299969-1_1 0 19 121291 1 22M * 0 0 CGAGCGCTGCGACATTTGAGCG * HI:i:0 MD:Z:0A0A2T17 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|-1|22M|0A0A2T17 -67825-4_1 0 19 121291 255 22M * 0 0 AAAGTGCTGCGACATTTGAGCG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|-1|22M|22 -90583-3_1 0 19 121291 255 22M * 0 0 AAATTGCTGCGACATTTGAGCG * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|-1|22M|3G18 -629861-1_1 0 19 121291 1 23M * 0 0 AGAGTGCTGCGACATTTGAGCGA * HI:i:0 MD:Z:1A20T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|0|23M|1A20T0 -120521-2_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|22T -739110-1_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|0|23M|23 -270338-1_1 0 19 121291 255 23M * 0 0 AAATTGCTGCGACATTTGAGCGT * MD:Z:3G19 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|3G19 -267649-1_1 0 19 121292 255 21M1I1M * 0 0 AAGTGCTGCGACATTTGAGCGAT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|1|0|21M1I1M|23 -313132-1_1 0 19 121292 255 22M * 0 0 AAGTGCTGCGACATTTGAGCGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|1|0|22M|22 -270337-1_1 0 19 121292 1 4M1I18M * 0 0 AACTTGCTGCGACATTTGAGCGT * HI:i:0 MD:Z:2G19 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|1|0|4M1I18M|2G19 -188149-2_1 0 19 122108 255 23M * 0 0 GAAGTGCTTCGATTTTGGGGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-373-3p|0|0|23M|23 -270393-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23 -610105-1_2 256 19 87 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 -610105-1_2 0 19 2571 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 -645839-1_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|20T -645839-1_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|20T -645839-1_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|20T0 -67830-4_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|21 -67830-4_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|21 -67830-4_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|21 -535182-1_3 256 19 89 1 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13 -535182-1_3 0 19 89 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13 -535182-1_3 0 19 2573 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13 -766380-1_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7 -766380-1_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7 -766380-1_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7 -67831-4_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|20 -67831-4_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|20 -67831-4_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|20 -270395-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|12A9 -270395-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|12A9 -270395-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|12A9 -773136-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|17A4 -773136-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|17A4 -773136-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|17A4 -102065-3_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|21C -102065-3_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|21C -102065-3_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|21C0 -37896-9_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|22 -37896-9_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|22 -37896-9_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|22 -334943-1_2 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0 -334943-1_2 0 19 2573 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0 -270396-1_3 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270401-1_2 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270396-1_3 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270401-1_2 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270396-1_3 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C0 -673650-1_2 256 19 89 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0 -673650-1_2 0 19 2573 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0 -150819-2_3 256 19 53 1 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|-1|21M|21 -150819-2_3 0 19 53 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|-1|21M|21 -150819-2_3 0 19 2537 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|-1|21M|21 -270402-1_3 0 19 53 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|-2|20M|20 -270402-1_3 256 19 53 1 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|-2|20M|20 -270402-1_3 0 19 2537 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|-2|20M|20 -752875-1_3 256 19 53 1 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|0|22M|22 -752875-1_3 0 19 53 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|0|22M|22 -752875-1_3 0 19 2537 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|0|22M|22 -369314-1_3 0 19 12413 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-515-3p|0|-1|21M|21 -369314-1_3 256 19 12413 1 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-515-3p|0|-1|21M|21 -369314-1_3 0 19 18419 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-515-3p|0|-1|21M|21 -54840-6_3 0 19 90116 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516a-5p|0|-1|22M|22 -54840-6_3 256 19 90116 1 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516a-5p|0|-1|22M|22 -54840-6_3 0 19 94508 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516a-5p|0|-1|22M|22 -423555-1_3 256 19 90117 1 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516a-5p|1|-1|21M|21 -423555-1_3 0 19 90117 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516a-5p|1|-1|21M|21 -423555-1_3 0 19 94509 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516a-5p|1|-1|21M|21 -270365-1_3 0 19 58817 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C -270365-1_3 0 19 70220 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C -270365-1_3 256 19 58817 1 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C0 -270366-1_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11 -270366-1_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11 -270366-1_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11 -86082-3_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|22 -86082-3_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|22 -86082-3_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|22 -270359-1_5 0 19 45641 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:1 YW:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 0 19 54440 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:2 YW:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 0 19 74691 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:4 YW:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 256 19 54440 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0 -270359-1_5 256 19 74691 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0 -752904-1_3 0 19 45646 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -752904-1_3 256 19 54445 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -752904-1_3 256 19 74696 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -105051-3_3 0 19 45646 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -105051-3_3 256 19 54445 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -105051-3_3 256 19 74696 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -120530-2_3 256 19 45681 1 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517a-3p|0|-1|21M|21 -120530-2_3 0 19 45681 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517a-3p|0|-1|21M|21 -67957-4_3 0 19 45681 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517a-3p|0|0|22M|22 -67957-4_3 256 19 45681 1 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517a-3p|0|0|22M|22 -120530-2_3 0 19 54478 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517b-3p|0|-1|21M|21 -67957-4_3 0 19 54478 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517b-3p|0|0|22M|22 -447402-1_1 0 19 36147 255 22M * 0 0 CAAAGCGCTCCCCTTTAGAGGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518b|0|0|22M|22 -270377-1_1 0 19 42119 255 21M * 0 0 CTCTGGAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|-1|21M|21 -751085-1_1 0 19 42119 255 20M * 0 0 CTCTGGAGGGAAGCACTTTA * MD:Z:19C NH:i:1 NM:i:1 YW:Z:hsa-miR-518c-5p|1|-2|20M|19C -270378-1_1 0 19 42119 255 22M * 0 0 CTCTGGAGGGAAGCACTTTCTG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|0|22M|22 -120527-2_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T -120527-2_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T0 -95680-3_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|21 -95680-3_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|21 -270379-1_5 256 19 68252 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-518d-5p|0|-1|21M|3T16T0 -139675-2_9 256 19 68252 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-2|20M|20 -139675-2_9 0 19 68252 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-2|20M|20 -531738-1_9 256 19 68252 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-3|19M|19 -531738-1_9 0 19 68252 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-3|19M|19 -270381-1_7 256 19 68252 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:6 YW:Z:hsa-miR-518d-5p|0|0|22M|22 -270381-1_7 0 19 68252 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:7 YW:Z:hsa-miR-518d-5p|0|0|22M|22 -270360-1_1 0 19 63251 255 21M * 0 0 AAAGCGCTTCCCTTCAGAGTG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518e-3p|0|0|21M|21 -676180-1_6 0 19 63213 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:4 YW:Z:hsa-miR-518e-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 63213 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-1|21M|21 -270361-1_11 0 19 63213 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-2|20M|19C -630277-1_11 0 19 63213 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-3|19M|19 -67687-4_11 0 19 63213 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|0|22M|22 -84523-3_11 0 19 63213 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|1|23M|23 -120527-2_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|20T -95680-3_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|21 -270379-1_5 0 19 33390 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|3T16T0 -139675-2_9 0 19 33390 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-2|20M|20 -531738-1_9 0 19 33390 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-3|19M|19 -347693-1_1 0 19 33390 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518f-5p|0|0|22M|22 -270348-1_3 0 19 85809 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270348-1_3 0 19 95757 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270348-1_3 256 19 95757 1 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270357-1_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCA * MD:Z:21T NH:i:1 NM:i:1 YW:Z:hsa-miR-519a-5p|-1|-1|22M|21T -58870-5_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-1|22M|22 -270354-1_1 0 19 85770 255 20M * 0 0 ACTCTAGAGGGAAGCGCTTT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-3|20M|20 -676180-1_6 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:6 YW:Z:hsa-miR-519a-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 85771 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-1|21M|21 -18915-24_11 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-1|21M|21 -270361-1_11 0 19 85771 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C -270361-1_11 256 19 85771 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C0 -630277-1_11 0 19 85771 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-3|19M|19 -630277-1_11 256 19 85771 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-3|19M|19 -67687-4_11 256 19 85771 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|0|22M|22 -67687-4_11 0 19 85771 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|0|22M|22 -84523-3_11 0 19 85771 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|1|23M|23 -84523-3_11 256 19 85771 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|1|23M|23 -676180-1_6 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:2 YW:Z:hsa-miR-519b-5p|0|-1|21M|19C0T0 -18915-24_11 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-1|21M|21 -18915-24_11 0 19 28585 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-1|21M|21 -270361-1_11 0 19 28585 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C -270361-1_11 256 19 28585 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C0 -630277-1_11 256 19 28585 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-3|19M|19 -630277-1_11 0 19 28585 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-3|19M|19 -67687-4_11 256 19 28585 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|0|22M|22 -67687-4_11 0 19 28585 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|0|22M|22 -84523-3_11 0 19 28585 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|1|23M|23 -84523-3_11 256 19 28585 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|1|23M|23 -676180-1_6 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 19844 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|21 -18915-24_11 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-1|21M|21 -270361-1_11 0 19 19844 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C -270361-1_11 256 19 19844 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C0 -630277-1_11 0 19 19844 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-3|19M|19 -630277-1_11 256 19 19844 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-3|19M|19 -67687-4_11 0 19 19844 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|0|22M|22 -67687-4_11 256 19 19844 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|0|22M|22 -84523-3_11 256 19 19844 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|1|23M|23 -84523-3_11 0 19 19844 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|1|23M|23 -270371-1_1 0 19 46760 255 21M * 0 0 CAAAGTGCCTCCCTTTAGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-1|21M|21 -153079-2_1 0 19 46760 255 20M * 0 0 CAAAGTGCCTCCCTTTAGAG * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-2|20M|20 -67829-4_1 0 19 24293 255 22M * 0 0 AAAGTGCTTCCCTTTGGACTGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-3p|0|0|22M|22 -655140-1_1 0 19 24293 255 22M * 0 0 AAATTGCTTCCCTTTGGACTGT * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|0|22M|3G18 -485300-1_1 0 19 24293 255 23M * 0 0 AAAGTGCTTCCCTTTGGACTGTA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|1|23M|22T -729311-1_1 0 19 24255 1 21M * 0 0 CTCCAGAGGGAAGTACTTTGA * HI:i:0 MD:Z:19C0T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|0|21M|19C0T0 -720817-1_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCG * MD:Z:20T NM:i:1 NH:i:1 HI:i:1 YW:Z:hsa-miR-520a-5p|0|0|21M|20T -120535-2_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-5p|0|0|21M|21 -228043-1_1 0 19 24255 1 19M1D2M * 0 0 CTCCAGAGGGAAGTACTTTAG * HI:i:0 MD:Z:19^C0T1 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 -609803-1_1 0 19 24255 1 19M1I3M * 0 0 CTCCAGAGGGAAGTACTTTGAAG * HI:i:0 MD:Z:19C0T1 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 -101076-3_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTAGA * HI:i:0 MD:Z:19^C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 -127441-2_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTTAA * HI:i:0 MD:Z:19^C1G0T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 -103161-3_1 0 19 24255 1 20M1D2M * 0 0 CTCCAGAGGGAAGTACTTTCGA * HI:i:0 MD:Z:20^T1T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 -478794-1_1 0 19 24255 1 23M * 0 0 CTCCAGAGGGAAGTACTTTAAGA * HI:i:0 MD:Z:19C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|23M|19C0T1T0 -744127-1_5 0 19 34626 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21 -744127-1_5 256 19 34626 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21 -120532-2_3 0 19 34627 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-520b-3p|0|1|22M|22 -744127-1_5 0 19 40865 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21 -744127-1_5 256 19 40865 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21 -120532-2_3 256 19 40866 1 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520c-3p|0|0|22M|22 -120532-2_3 0 19 40866 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520c-3p|0|0|22M|22 -120527-2_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T -120527-2_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T0 -95680-3_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|21 -95680-3_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|21 -270379-1_5 256 19 40828 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520c-5p|0|-1|21M|3T16T0 -139675-2_9 256 19 40828 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-2|20M|20 -139675-2_9 0 19 40828 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-2|20M|20 -531738-1_9 256 19 40828 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-3|19M|19 -531738-1_9 0 19 40828 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-3|19M|19 -270381-1_7 256 19 40828 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:3 YW:Z:hsa-miR-520c-5p|0|0|22M|22 -270381-1_7 0 19 40828 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:4 YW:Z:hsa-miR-520c-5p|0|0|22M|22 -361022-1_1 0 19 9124 255 21M * 0 0 AAAGTGCTTCCTTTTTGAGGG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520e-3p|0|0|21M|21 -772976-1_1 0 19 9089 1 7M1I9M * 0 0 AAAATGGGAAGCAGTTT * HI:i:0 MD:Z:2G13 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520e-5p|3|-3|7M1I9M|2G13 -270368-1_3 0 19 55581 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-520g-3p|1|-2|21M|21 -270369-1_1 0 19 55581 255 23M * 0 0 CAAAGTGCTTCCCTTTAGAGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-520g-3p|1|0|23M|23 -138559-2_2 0 19 55539 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 -270368-1_3 0 19 75927 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520h|1|0|21M|21 -270368-1_3 256 19 75927 1 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520h|1|0|21M|21 -270358-1_1 0 19 84624 1 22M * 0 0 AGAATGGTTCCCTTTAGAGTGT * MD:Z:1A20 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 YW:Z:hsa-miR-522-3p|0|0|22M|1A20 -676180-1_6 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:5 YW:Z:hsa-miR-522-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 84586 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-1|21M|21 -18915-24_11 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-1|21M|21 -270361-1_11 0 19 84586 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-2|20M|19C -270361-1_11 256 19 84586 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-2|20M|19C0 -630277-1_11 256 19 84586 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-3|19M|19 -630277-1_11 0 19 84586 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-3|19M|19 -67687-4_11 0 19 84586 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|0|22M|22 -67687-4_11 256 19 84586 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|0|22M|22 -84523-3_11 256 19 84586 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|1|23M|23 -84523-3_11 0 19 84586 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|1|23M|23 -676180-1_6 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:3 YW:Z:hsa-miR-523-5p|0|-1|21M|19C0T0 -18915-24_11 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-1|21M|21 -18915-24_11 0 19 31760 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-1|21M|21 -270361-1_11 0 19 31760 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-2|20M|19C -270361-1_11 256 19 31760 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-2|20M|19C0 -630277-1_11 256 19 31760 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-3|19M|19 -630277-1_11 0 19 31760 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-3|19M|19 -67687-4_11 256 19 31760 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|0|22M|22 -67687-4_11 0 19 31760 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|0|22M|22 -84523-3_11 0 19 31760 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|1|23M|23 -84523-3_11 256 19 31760 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|1|23M|23 -270375-1_1 0 19 44377 255 21M * 0 0 CTACAAAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-1|21M|21 -270376-1_1 0 19 44377 255 20M * 0 0 CTACAAAGGGAAGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-2|20M|20 -57516-5_1 0 19 30907 255 20M * 0 0 CTCCAGAGGGATGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|-1|20M|20 -102026-3_1 0 19 30907 255 21M * 0 0 CTCCAGAGGGATGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|0|21M|21 -120527-2_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T -120527-2_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T -120527-2_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0 -120527-2_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0 -95680-3_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -270379-1_5 256 19 39626 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0 -270379-1_5 256 19 60288 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0 -139675-2_9 0 19 39626 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 256 19 39626 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 0 19 60288 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 256 19 60288 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -531738-1_9 0 19 39626 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 256 19 39626 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 0 19 60288 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 256 19 60288 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -270381-1_7 0 19 39626 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:1 YW:Z:hsa-miR-526a-5p|0|0|22M|22 -270381-1_7 256 19 39626 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:2 YW:Z:hsa-miR-526a-5p|0|0|22M|22 -270381-1_7 0 19 60288 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:5 YW:Z:hsa-miR-526a-5p|0|0|22M|22 +709268-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC +528546-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22|TCAAAACTGAGGGGCATTTTCT +270342-1_1 0 19 121040 255 20M * 0 0 ACTCAAACTGTGGGGGCACT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-371a-5p|0|0|20M|20|ACTCAAACTGTGGGGGCACT +840419-1_1 0 19 121040 1 23M * 0 0 ACTCAAACTGTGGGGGCCCTTAG * HI:i:0 MD:Z:17A3T0C0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG +120522-2_1 16 19 121038 255 22M * 0 0 GCACTCAAACTGTGGGGGCACT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT +299969-1_1 0 19 121291 1 22M * 0 0 CGAGCGCTGCGACATTTGAGCG * HI:i:0 MD:Z:0A0A2T17 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG +67825-4_1 0 19 121291 255 22M * 0 0 AAAGTGCTGCGACATTTGAGCG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG +90583-3_1 0 19 121291 255 22M * 0 0 AAATTGCTGCGACATTTGAGCG * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG +629861-1_1 0 19 121291 1 23M * 0 0 AGAGTGCTGCGACATTTGAGCGA * HI:i:0 MD:Z:1A20T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA +120521-2_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA +739110-1_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|0|23M|23|AAAGTGCTGCGACATTTGAGCGT +270338-1_1 0 19 121291 255 23M * 0 0 AAATTGCTGCGACATTTGAGCGT * MD:Z:3G19 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT +267649-1_1 0 19 121292 255 21M1I1M * 0 0 AAGTGCTGCGACATTTGAGCGAT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT +313132-1_1 0 19 121292 255 22M * 0 0 AAGTGCTGCGACATTTGAGCGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT +270337-1_1 0 19 121292 1 4M1I18M * 0 0 AACTTGCTGCGACATTTGAGCGT * HI:i:0 MD:Z:2G19 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT +188149-2_1 0 19 122108 255 23M * 0 0 GAAGTGCTTCGATTTTGGGGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-373-3p|0|0|23M|23|GAAGTGCTTCGATTTTGGGGTGT +270393-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23|TTTCAAGCCAGGGGGCGTTTTTC +610105-1_2 256 19 87 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA +610105-1_2 0 19 2571 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA +645839-1_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA +645839-1_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA +645839-1_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA +67830-4_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +67830-4_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +67830-4_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +535182-1_3 256 19 89 1 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +535182-1_3 0 19 89 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +535182-1_3 0 19 2573 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +766380-1_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +766380-1_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +766380-1_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +67831-4_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +67831-4_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +67831-4_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +270395-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +270395-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +270395-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +773136-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +773136-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +773136-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +102065-3_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT +102065-3_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT +102065-3_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT +37896-9_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +37896-9_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +37896-9_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +334943-1_2 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG +334943-1_2 0 19 2573 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG +270396-1_3 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT +270401-1_2 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA +270396-1_3 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT +270401-1_2 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA +270396-1_3 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT +673650-1_2 256 19 89 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT +673650-1_2 0 19 2573 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT +150819-2_3 256 19 53 1 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +150819-2_3 0 19 53 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +150819-2_3 0 19 2537 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +270402-1_3 0 19 53 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +270402-1_3 256 19 53 1 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +270402-1_3 0 19 2537 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +752875-1_3 256 19 53 1 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +752875-1_3 0 19 53 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +752875-1_3 0 19 2537 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +369314-1_3 0 19 12413 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +369314-1_3 256 19 12413 1 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +369314-1_3 0 19 18419 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +54840-6_3 0 19 90116 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +54840-6_3 256 19 90116 1 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +54840-6_3 0 19 94508 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +423555-1_3 256 19 90117 1 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +423555-1_3 0 19 90117 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +423555-1_3 0 19 94509 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +270365-1_3 0 19 58817 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA +270365-1_3 0 19 70220 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA +270365-1_3 256 19 58817 1 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA +270366-1_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +270366-1_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +270366-1_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +86082-3_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +86082-3_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +86082-3_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +270359-1_5 0 19 45641 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:1 YW:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 0 19 54440 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:2 YW:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 0 19 74691 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:4 YW:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 256 19 54440 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 256 19 74691 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA +752904-1_3 0 19 45646 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +752904-1_3 256 19 54445 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +752904-1_3 256 19 74696 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +105051-3_3 0 19 45646 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +105051-3_3 256 19 54445 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +105051-3_3 256 19 74696 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +120530-2_3 256 19 45681 1 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +120530-2_3 0 19 45681 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +67957-4_3 0 19 45681 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517a-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +67957-4_3 256 19 45681 1 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517a-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +120530-2_3 0 19 54478 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +67957-4_3 0 19 54478 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517b-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +447402-1_1 0 19 36147 255 22M * 0 0 CAAAGCGCTCCCCTTTAGAGGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518b|0|0|22M|22|CAAAGCGCTCCCCTTTAGAGGT +270377-1_1 0 19 42119 255 21M * 0 0 CTCTGGAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT +751085-1_1 0 19 42119 255 20M * 0 0 CTCTGGAGGGAAGCACTTTA * MD:Z:19C NH:i:1 NM:i:1 YW:Z:hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA +270378-1_1 0 19 42119 255 22M * 0 0 CTCTGGAGGGAAGCACTTTCTG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG +120527-2_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 68252 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 256 19 68252 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 0 19 68252 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +531738-1_9 256 19 68252 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 0 19 68252 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +270381-1_7 256 19 68252 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:6 YW:Z:hsa-miR-518d-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 68252 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:7 YW:Z:hsa-miR-518d-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270360-1_1 0 19 63251 255 21M * 0 0 AAAGCGCTTCCCTTCAGAGTG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518e-3p|0|0|21M|21|AAAGCGCTTCCCTTCAGAGTG +676180-1_6 0 19 63213 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:4 YW:Z:hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 63213 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 63213 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 63213 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 63213 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 63213 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +120527-2_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +95680-3_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 0 19 33390 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 0 19 33390 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +531738-1_9 0 19 33390 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +347693-1_1 0 19 33390 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518f-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTC +270348-1_3 0 19 85809 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270348-1_3 0 19 95757 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270348-1_3 256 19 95757 1 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270357-1_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCA * MD:Z:21T NH:i:1 NM:i:1 YW:Z:hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA +58870-5_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT +270354-1_1 0 19 85770 255 20M * 0 0 ACTCTAGAGGGAAGCGCTTT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT +676180-1_6 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:6 YW:Z:hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 85771 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 85771 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 85771 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 85771 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 256 19 85771 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 85771 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 85771 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 85771 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 85771 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:2 YW:Z:hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 0 19 28585 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 28585 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 28585 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 28585 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 28585 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 28585 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 28585 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 28585 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 28585 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 19844 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 19844 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 19844 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 19844 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 256 19 19844 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 19844 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 256 19 19844 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 256 19 19844 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 0 19 19844 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +270371-1_1 0 19 46760 255 21M * 0 0 CAAAGTGCCTCCCTTTAGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT +153079-2_1 0 19 46760 255 20M * 0 0 CAAAGTGCCTCCCTTTAGAG * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG +67829-4_1 0 19 24293 255 22M * 0 0 AAAGTGCTTCCCTTTGGACTGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-3p|0|0|22M|22|AAAGTGCTTCCCTTTGGACTGT +655140-1_1 0 19 24293 255 22M * 0 0 AAATTGCTTCCCTTTGGACTGT * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT +485300-1_1 0 19 24293 255 23M * 0 0 AAAGTGCTTCCCTTTGGACTGTA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA +729311-1_1 0 19 24255 1 21M * 0 0 CTCCAGAGGGAAGTACTTTGA * HI:i:0 MD:Z:19C0T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA +720817-1_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCG * MD:Z:20T NM:i:1 NH:i:1 HI:i:1 YW:Z:hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG +120535-2_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-5p|0|0|21M|21|CTCCAGAGGGAAGTACTTTCT +228043-1_1 0 19 24255 1 19M1D2M * 0 0 CTCCAGAGGGAAGTACTTTAG * HI:i:0 MD:Z:19^C0T1 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG +609803-1_1 0 19 24255 1 19M1I3M * 0 0 CTCCAGAGGGAAGTACTTTGAAG * HI:i:0 MD:Z:19C0T1 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG +101076-3_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTAGA * HI:i:0 MD:Z:19^C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA +127441-2_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTTAA * HI:i:0 MD:Z:19^C1G0T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA +103161-3_1 0 19 24255 1 20M1D2M * 0 0 CTCCAGAGGGAAGTACTTTCGA * HI:i:0 MD:Z:20^T1T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA +478794-1_1 0 19 24255 1 23M * 0 0 CTCCAGAGGGAAGTACTTTAAGA * HI:i:0 MD:Z:19C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA +744127-1_5 0 19 34626 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG +744127-1_5 256 19 34626 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG +120532-2_3 0 19 34627 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT +744127-1_5 0 19 40865 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG +744127-1_5 256 19 40865 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG +120532-2_3 256 19 40866 1 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520c-3p|0|0|22M|22|AAAGTGCTTCCTTTTAGAGGGT +120532-2_3 0 19 40866 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520c-3p|0|0|22M|22|AAAGTGCTTCCTTTTAGAGGGT +120527-2_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 40828 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 256 19 40828 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +139675-2_9 0 19 40828 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +531738-1_9 256 19 40828 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +531738-1_9 0 19 40828 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +270381-1_7 256 19 40828 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:3 YW:Z:hsa-miR-520c-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 40828 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:4 YW:Z:hsa-miR-520c-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +361022-1_1 0 19 9124 255 21M * 0 0 AAAGTGCTTCCTTTTTGAGGG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520e-3p|0|0|21M|21|AAAGTGCTTCCTTTTTGAGGG +772976-1_1 0 19 9089 1 7M1I9M * 0 0 AAAATGGGAAGCAGTTT * HI:i:0 MD:Z:2G13 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT +270368-1_3 0 19 55581 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT +270369-1_1 0 19 55581 255 23M * 0 0 CAAAGTGCTTCCCTTTAGAGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT +138559-2_2 0 19 55539 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT +270368-1_3 0 19 75927 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT +270368-1_3 256 19 75927 1 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT +270358-1_1 0 19 84624 1 22M * 0 0 AGAATGGTTCCCTTTAGAGTGT * MD:Z:1A20 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 YW:Z:hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT +676180-1_6 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:5 YW:Z:hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 84586 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 84586 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 84586 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 84586 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 84586 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 84586 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 256 19 84586 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 256 19 84586 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 0 19 84586 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:3 YW:Z:hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 0 19 31760 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 31760 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 31760 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 31760 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 31760 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 31760 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 31760 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 31760 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 31760 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +270375-1_1 0 19 44377 255 21M * 0 0 CTACAAAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270376-1_1 0 19 44377 255 20M * 0 0 CTACAAAGGGAAGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC +57516-5_1 0 19 30907 255 20M * 0 0 CTCCAGAGGGATGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC +102026-3_1 0 19 30907 255 21M * 0 0 CTCCAGAGGGATGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|0|21M|21|CTCCAGAGGGATGCACTTTCT +120527-2_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 39626 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA +270379-1_5 256 19 60288 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA +139675-2_9 0 19 39626 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 256 19 39626 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 0 19 60288 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 256 19 60288 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +531738-1_9 0 19 39626 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 256 19 39626 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 0 19 60288 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 256 19 60288 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +270381-1_7 0 19 39626 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:1 YW:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 256 19 39626 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:2 YW:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 60288 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:5 YW:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG diff --git a/scripts/tests/files/in_aln_tag_XN.sam b/scripts/tests/files/in_aln_tag_XN.sam index ce7d13d..0ba6745 100644 --- a/scripts/tests/files/in_aln_tag_XN.sam +++ b/scripts/tests/files/in_aln_tag_XN.sam @@ -3,257 +3,266 @@ @PG ID:samtools PN:samtools VN:1.16.1 CL:samtools sort -n -o results/test_lib/header_sorted_catMappings.sam results/test_lib/concatenated_header_catMappings.sam @PG ID:samtools.1 PN:samtools PP:samtools VN:1.16.1 CL:samtools view -H results/test_lib/removeMultimappers.sam @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:samtools view -H results/test_lib/premir_intersectedAlignments.sam -@PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.16.1 CL:samtools sort -t YW -O SAM results/test_lib/mirna_intersecting_tag.sam -709268-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-1323|0|-1|21M|21 -528546-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-1323|0|0|22M|22 -270342-1_1 0 19 121040 255 20M * 0 0 ACTCAAACTGTGGGGGCACT * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-371a-5p|0|0|20M|20 -840419-1_1 0 19 121040 1 23M * 0 0 ACTCAAACTGTGGGGGCCCTTAG * HI:i:0 MD:Z:17A3T0C0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-371a-5p|0|3|23M|17A3T0C0 -120522-2_1 16 19 121038 255 22M * 0 0 GCACTCAAACTGTGGGGGCACT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-371b-3p|0|-1|22M|22 -299969-1_1 0 19 121291 1 22M * 0 0 CGAGCGCTGCGACATTTGAGCG * HI:i:0 MD:Z:0A0A2T17 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-372-3p|0|-1|22M|0A0A2T17 -67825-4_1 0 19 121291 255 22M * 0 0 AAAGTGCTGCGACATTTGAGCG * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-372-3p|0|-1|22M|22 -90583-3_1 0 19 121291 255 22M * 0 0 AAATTGCTGCGACATTTGAGCG * MD:Z:3G18 NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|0|-1|22M|3G18 -629861-1_1 0 19 121291 1 23M * 0 0 AGAGTGCTGCGACATTTGAGCGA * HI:i:0 MD:Z:1A20T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-372-3p|0|0|23M|1A20T0 -120521-2_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGA * MD:Z:22T NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|0|0|23M|22T -739110-1_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGT * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-372-3p|0|0|23M|23 -270338-1_1 0 19 121291 255 23M * 0 0 AAATTGCTGCGACATTTGAGCGT * MD:Z:3G19 NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|0|0|23M|3G19 -267649-1_1 0 19 121292 255 21M1I1M * 0 0 AAGTGCTGCGACATTTGAGCGAT * MD:Z:23 NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|1|0|21M1I1M|23 -313132-1_1 0 19 121292 255 22M * 0 0 AAGTGCTGCGACATTTGAGCGT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-372-3p|1|0|22M|22 -270337-1_1 0 19 121292 1 4M1I18M * 0 0 AACTTGCTGCGACATTTGAGCGT * HI:i:0 MD:Z:2G19 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-372-3p|1|0|4M1I18M|2G19 -188149-2_1 0 19 122108 255 23M * 0 0 GAAGTGCTTCGATTTTGGGGTGT * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-373-3p|0|0|23M|23 -270393-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-498-5p|0|0|23M|23 -610105-1_2 256 19 87 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 -610105-1_2 0 19 2571 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 -645839-1_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-1|21M|20T -645839-1_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-1|21M|20T -645839-1_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-1|21M|20T0 -67830-4_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-1|21M|21 -67830-4_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-1|21M|21 -67830-4_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-1|21M|21 -535182-1_3 256 19 89 1 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-1|21M|7G13 -535182-1_3 0 19 89 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-1|21M|7G13 -535182-1_3 0 19 2573 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-1|21M|7G13 -766380-1_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-2|20M|12A7 -766380-1_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-2|20M|12A7 -766380-1_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-2|20M|12A7 -67831-4_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-2|20M|20 -67831-4_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-2|20M|20 -67831-4_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-2|20M|20 -270395-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|12A9 -270395-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|12A9 -270395-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|12A9 -773136-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|17A4 -773136-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|17A4 -773136-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|17A4 -102065-3_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|21C -102065-3_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|21C -102065-3_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|21C0 -37896-9_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|22 -37896-9_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|22 -37896-9_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|22 -334943-1_2 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|21C0C0 -334943-1_2 0 19 2573 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|21C0C0 -270396-1_3 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|22C -270401-1_2 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|22C -270396-1_3 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|1|23M|22C -270401-1_2 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|22C -270396-1_3 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|22C0 -673650-1_2 256 19 89 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|3T18C0 -673650-1_2 0 19 2573 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|3T18C0 -150819-2_3 256 19 53 1 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-5p|1|-1|21M|21 -150819-2_3 0 19 53 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-5p|1|-1|21M|21 -150819-2_3 0 19 2537 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-5p|1|-1|21M|21 -270402-1_3 0 19 53 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-5p|1|-2|20M|20 -270402-1_3 256 19 53 1 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-5p|1|-2|20M|20 -270402-1_3 0 19 2537 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-5p|1|-2|20M|20 -752875-1_3 256 19 53 1 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-5p|1|0|22M|22 -752875-1_3 0 19 53 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-5p|1|0|22M|22 -752875-1_3 0 19 2537 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-5p|1|0|22M|22 -369314-1_3 0 19 12413 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-515-3p|0|-1|21M|21 -369314-1_3 256 19 12413 1 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-515-3p|0|-1|21M|21 -369314-1_3 0 19 18419 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-515-3p|0|-1|21M|21 -54840-6_3 0 19 90116 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516a-5p|0|-1|22M|22 -54840-6_3 256 19 90116 1 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-516a-5p|0|-1|22M|22 -54840-6_3 0 19 94508 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-516a-5p|0|-1|22M|22 -423555-1_3 256 19 90117 1 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516a-5p|1|-1|21M|21 -423555-1_3 0 19 90117 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-516a-5p|1|-1|21M|21 -423555-1_3 0 19 94509 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-516a-5p|1|-1|21M|21 -270365-1_3 0 19 58817 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-516b-5p|0|-3|19M|18C -270365-1_3 0 19 70220 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-516b-5p|0|-3|19M|18C -270365-1_3 256 19 58817 1 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516b-5p|0|-3|19M|18C0 -270366-1_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516b-5p|0|0|22M|10A11 -270366-1_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-516b-5p|0|0|22M|10A11 -270366-1_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-516b-5p|0|0|22M|10A11 -86082-3_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516b-5p|0|0|22M|22 -86082-3_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-516b-5p|0|0|22M|22 -86082-3_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-516b-5p|0|0|22M|22 -270359-1_5 0 19 45641 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:1 XN:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 0 19 54440 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:2 XN:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 0 19 74691 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:4 XN:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 256 19 54440 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 XN:Z:hsa-miR-517-5p|-1|0|23M|22T0 -270359-1_5 256 19 74691 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 XN:Z:hsa-miR-517-5p|-1|0|23M|22T0 -752904-1_3 0 19 45646 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -752904-1_3 256 19 54445 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -752904-1_3 256 19 74696 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -105051-3_3 0 19 45646 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -105051-3_3 256 19 54445 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -105051-3_3 256 19 74696 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -120530-2_3 256 19 45681 1 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517a-3p|0|-1|21M|21 -120530-2_3 0 19 45681 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517a-3p|0|-1|21M|21 -67957-4_3 0 19 45681 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517a-3p|0|0|22M|22 -67957-4_3 256 19 45681 1 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517a-3p|0|0|22M|22 -120530-2_3 0 19 54478 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517b-3p|0|-1|21M|21 -67957-4_3 0 19 54478 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517b-3p|0|0|22M|22 -447402-1_1 0 19 36147 255 22M * 0 0 CAAAGCGCTCCCCTTTAGAGGT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-518b|0|0|22M|22 -270377-1_1 0 19 42119 255 21M * 0 0 CTCTGGAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-518c-5p|1|-1|21M|21 -751085-1_1 0 19 42119 255 20M * 0 0 CTCTGGAGGGAAGCACTTTA * MD:Z:19C NH:i:1 NM:i:1 XN:Z:hsa-miR-518c-5p|1|-2|20M|19C -270378-1_1 0 19 42119 255 22M * 0 0 CTCTGGAGGGAAGCACTTTCTG * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-518c-5p|1|0|22M|22 -120527-2_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-1|21M|20T -120527-2_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-1|21M|20T0 -95680-3_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-1|21M|21 -95680-3_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-1|21M|21 -270379-1_5 256 19 68252 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 XN:Z:hsa-miR-518d-5p|0|-1|21M|3T16T0 -139675-2_9 256 19 68252 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-2|20M|20 -139675-2_9 0 19 68252 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-2|20M|20 -531738-1_9 256 19 68252 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-3|19M|19 -531738-1_9 0 19 68252 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-3|19M|19 -270381-1_7 256 19 68252 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:6 XN:Z:hsa-miR-518d-5p|0|0|22M|22 -270381-1_7 0 19 68252 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:7 XN:Z:hsa-miR-518d-5p|0|0|22M|22 -270360-1_1 0 19 63251 255 21M * 0 0 AAAGCGCTTCCCTTCAGAGTG * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-518e-3p|0|0|21M|21 -676180-1_6 0 19 63213 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:4 XN:Z:hsa-miR-518e-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 63213 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|-1|21M|21 -270361-1_11 0 19 63213 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|-2|20M|19C -630277-1_11 0 19 63213 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|-3|19M|19 -67687-4_11 0 19 63213 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|0|22M|22 -84523-3_11 0 19 63213 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|1|23M|23 -120527-2_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-1|21M|20T -95680-3_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-1|21M|21 -270379-1_5 0 19 33390 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-1|21M|3T16T0 -139675-2_9 0 19 33390 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-2|20M|20 -531738-1_9 0 19 33390 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-3|19M|19 -347693-1_1 0 19 33390 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-518f-5p|0|0|22M|22 -270348-1_3 0 19 85809 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270348-1_3 0 19 95757 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270348-1_3 256 19 95757 1 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270357-1_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCA * MD:Z:21T NH:i:1 NM:i:1 XN:Z:hsa-miR-519a-5p|-1|-1|22M|21T -58870-5_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-519a-5p|-1|-1|22M|22 -270354-1_1 0 19 85770 255 20M * 0 0 ACTCTAGAGGGAAGCGCTTT * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-519a-5p|-1|-3|20M|20 -676180-1_6 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:6 XN:Z:hsa-miR-519a-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 85771 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|-1|21M|21 -18915-24_11 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|-1|21M|21 -270361-1_11 0 19 85771 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|-2|20M|19C -270361-1_11 256 19 85771 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|-2|20M|19C0 -630277-1_11 0 19 85771 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|-3|19M|19 -630277-1_11 256 19 85771 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|-3|19M|19 -67687-4_11 256 19 85771 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|0|22M|22 -67687-4_11 0 19 85771 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|0|22M|22 -84523-3_11 0 19 85771 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|1|23M|23 -84523-3_11 256 19 85771 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|1|23M|23 -676180-1_6 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:2 XN:Z:hsa-miR-519b-5p|0|-1|21M|19C0T0 -18915-24_11 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|-1|21M|21 -18915-24_11 0 19 28585 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|-1|21M|21 -270361-1_11 0 19 28585 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|-2|20M|19C -270361-1_11 256 19 28585 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|-2|20M|19C0 -630277-1_11 256 19 28585 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|-3|19M|19 -630277-1_11 0 19 28585 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|-3|19M|19 -67687-4_11 256 19 28585 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|0|22M|22 -67687-4_11 0 19 28585 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|0|22M|22 -84523-3_11 0 19 28585 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|1|23M|23 -84523-3_11 256 19 28585 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|1|23M|23 -676180-1_6 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 19844 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-1|21M|21 -18915-24_11 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|-1|21M|21 -270361-1_11 0 19 19844 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|-2|20M|19C -270361-1_11 256 19 19844 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-2|20M|19C0 -630277-1_11 0 19 19844 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-3|19M|19 -630277-1_11 256 19 19844 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|-3|19M|19 -67687-4_11 0 19 19844 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|0|22M|22 -67687-4_11 256 19 19844 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|0|22M|22 -84523-3_11 256 19 19844 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|1|23M|23 -84523-3_11 0 19 19844 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|1|23M|23 -270371-1_1 0 19 46760 255 21M * 0 0 CAAAGTGCCTCCCTTTAGAGT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-519d-3p|0|-1|21M|21 -153079-2_1 0 19 46760 255 20M * 0 0 CAAAGTGCCTCCCTTTAGAG * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-519d-3p|0|-2|20M|20 -67829-4_1 0 19 24293 255 22M * 0 0 AAAGTGCTTCCCTTTGGACTGT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-520a-3p|0|0|22M|22 -655140-1_1 0 19 24293 255 22M * 0 0 AAATTGCTTCCCTTTGGACTGT * MD:Z:3G18 NH:i:1 NM:i:1 XN:Z:hsa-miR-520a-3p|0|0|22M|3G18 -485300-1_1 0 19 24293 255 23M * 0 0 AAAGTGCTTCCCTTTGGACTGTA * MD:Z:22T NH:i:1 NM:i:1 XN:Z:hsa-miR-520a-3p|0|1|23M|22T -729311-1_1 0 19 24255 1 21M * 0 0 CTCCAGAGGGAAGTACTTTGA * HI:i:0 MD:Z:19C0T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|0|21M|19C0T0 -720817-1_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCG * MD:Z:20T NM:i:1 NH:i:1 HI:i:1 XN:Z:hsa-miR-520a-5p|0|0|21M|20T -120535-2_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-520a-5p|0|0|21M|21 -228043-1_1 0 19 24255 1 19M1D2M * 0 0 CTCCAGAGGGAAGTACTTTAG * HI:i:0 MD:Z:19^C0T1 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 -609803-1_1 0 19 24255 1 19M1I3M * 0 0 CTCCAGAGGGAAGTACTTTGAAG * HI:i:0 MD:Z:19C0T1 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 -101076-3_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTAGA * HI:i:0 MD:Z:19^C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 -127441-2_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTTAA * HI:i:0 MD:Z:19^C1G0T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 -103161-3_1 0 19 24255 1 20M1D2M * 0 0 CTCCAGAGGGAAGTACTTTCGA * HI:i:0 MD:Z:20^T1T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 -478794-1_1 0 19 24255 1 23M * 0 0 CTCCAGAGGGAAGTACTTTAAGA * HI:i:0 MD:Z:19C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|23M|19C0T1T0 -744127-1_5 0 19 34626 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:2 XN:Z:hsa-miR-520b-3p|-1|-1|21M|21 -744127-1_5 256 19 34626 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 XN:Z:hsa-miR-520b-3p|-1|-1|21M|21 -120532-2_3 0 19 34627 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-520b-3p|0|1|22M|22 -744127-1_5 0 19 40865 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:4 XN:Z:hsa-miR-520c-3p|-1|-2|21M|21 -744127-1_5 256 19 40865 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 XN:Z:hsa-miR-520c-3p|-1|-2|21M|21 -120532-2_3 256 19 40866 1 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-520c-3p|0|0|22M|22 -120532-2_3 0 19 40866 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-520c-3p|0|0|22M|22 -120527-2_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-1|21M|20T -120527-2_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-1|21M|20T0 -95680-3_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-1|21M|21 -95680-3_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-1|21M|21 -270379-1_5 256 19 40828 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 XN:Z:hsa-miR-520c-5p|0|-1|21M|3T16T0 -139675-2_9 256 19 40828 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-2|20M|20 -139675-2_9 0 19 40828 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-2|20M|20 -531738-1_9 256 19 40828 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-3|19M|19 -531738-1_9 0 19 40828 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-3|19M|19 -270381-1_7 256 19 40828 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:3 XN:Z:hsa-miR-520c-5p|0|0|22M|22 -270381-1_7 0 19 40828 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:4 XN:Z:hsa-miR-520c-5p|0|0|22M|22 -361022-1_1 0 19 9124 255 21M * 0 0 AAAGTGCTTCCTTTTTGAGGG * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-520e-3p|0|0|21M|21 -772976-1_1 0 19 9089 1 7M1I9M * 0 0 AAAATGGGAAGCAGTTT * HI:i:0 MD:Z:2G13 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520e-5p|3|-3|7M1I9M|2G13 -270368-1_3 0 19 55581 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-520g-3p|1|-2|21M|21 -270369-1_1 0 19 55581 255 23M * 0 0 CAAAGTGCTTCCCTTTAGAGTGT * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-520g-3p|1|0|23M|23 -138559-2_2 0 19 55539 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 -270368-1_3 0 19 75927 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-520h|1|0|21M|21 -270368-1_3 256 19 75927 1 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-520h|1|0|21M|21 -270358-1_1 0 19 84624 1 22M * 0 0 AGAATGGTTCCCTTTAGAGTGT * MD:Z:1A20 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 XN:Z:hsa-miR-522-3p|0|0|22M|1A20 -676180-1_6 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:5 XN:Z:hsa-miR-522-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 84586 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|-1|21M|21 -18915-24_11 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|-1|21M|21 -270361-1_11 0 19 84586 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|-2|20M|19C -270361-1_11 256 19 84586 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|-2|20M|19C0 -630277-1_11 256 19 84586 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|-3|19M|19 -630277-1_11 0 19 84586 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|-3|19M|19 -67687-4_11 0 19 84586 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|0|22M|22 -67687-4_11 256 19 84586 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|0|22M|22 -84523-3_11 256 19 84586 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|1|23M|23 -84523-3_11 0 19 84586 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|1|23M|23 -676180-1_6 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:3 XN:Z:hsa-miR-523-5p|0|-1|21M|19C0T0 -18915-24_11 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|-1|21M|21 -18915-24_11 0 19 31760 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|-1|21M|21 -270361-1_11 0 19 31760 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|-2|20M|19C -270361-1_11 256 19 31760 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|-2|20M|19C0 -630277-1_11 256 19 31760 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|-3|19M|19 -630277-1_11 0 19 31760 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|-3|19M|19 -67687-4_11 256 19 31760 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|0|22M|22 -67687-4_11 0 19 31760 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|0|22M|22 -84523-3_11 0 19 31760 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|1|23M|23 -84523-3_11 256 19 31760 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|1|23M|23 -270375-1_1 0 19 44377 255 21M * 0 0 CTACAAAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-524-5p|0|-1|21M|21 -270376-1_1 0 19 44377 255 20M * 0 0 CTACAAAGGGAAGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-524-5p|0|-2|20M|20 -57516-5_1 0 19 30907 255 20M * 0 0 CTCCAGAGGGATGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-525-5p|0|-1|20M|20 -102026-3_1 0 19 30907 255 21M * 0 0 CTCCAGAGGGATGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-525-5p|0|0|21M|21 -120527-2_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T -120527-2_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T -120527-2_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T0 -120527-2_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T0 -95680-3_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-1|21M|21 -270379-1_5 256 19 39626 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0 -270379-1_5 256 19 60288 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:4 XN:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0 -139675-2_9 0 19 39626 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 256 19 39626 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 0 19 60288 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 256 19 60288 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-2|20M|20 -531738-1_9 0 19 39626 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 256 19 39626 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 0 19 60288 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 256 19 60288 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-3|19M|19 -270381-1_7 0 19 39626 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:1 XN:Z:hsa-miR-526a-5p|0|0|22M|22 -270381-1_7 256 19 39626 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:2 XN:Z:hsa-miR-526a-5p|0|0|22M|22 -270381-1_7 0 19 60288 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:5 XN:Z:hsa-miR-526a-5p|0|0|22M|22 +@PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.16.1 CL:samtools sort -t XN -O SAM results/test_lib/mirna_intersecting_tag.sam +256497-1_1 0 19 9096 1 4M1I9M1I2M * 0 0 AAGCCAGTTTCTGTCTG * HI:i:0 MD:Z:15 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z: +391978-1_2 256 19 12384 1 3M1I2M1I14M * 0 0 AAGCAACAGCACTTTCTGTAG * MD:Z:17T1 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z: +391978-1_2 0 19 18390 1 3M1I2M1I14M * 0 0 AAGCAACAGCACTTTCTGTAG * MD:Z:17T1 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z: +705321-1_1 0 19 24304 1 16M * 0 0 CTTTGGACTGTTTCTG * MD:Z:14G1 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 XN:Z: +615330-1_1 0 19 42114 1 4M1I16M * 0 0 TCACAACTCTGGAGGGAAGCA * HI:i:0 MD:Z:1G2T15 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z: +623283-1_1 0 19 42116 1 2M1I16M * 0 0 ACAACTCTGGAGGGAAGCA * HI:i:0 MD:Z:2T15 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z: +445515-1_1 0 19 53506 1 9M1D7M * 0 0 AAGAAAGTGTTCTCTA * HI:i:0 MD:Z:9^C6T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z: +138559-2_2 256 19 75885 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z: +641705-1_1 0 19 121288 1 9M1I6M * 0 0 TGGAAAGTGGCTGAGA * HI:i:0 MD:Z:12C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z: +709268-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC +528546-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-1323|0|0|22M|22|TCAAAACTGAGGGGCATTTTCT +270342-1_1 0 19 121040 255 20M * 0 0 ACTCAAACTGTGGGGGCACT * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-371a-5p|0|0|20M|20|ACTCAAACTGTGGGGGCACT +840419-1_1 0 19 121040 1 23M * 0 0 ACTCAAACTGTGGGGGCCCTTAG * HI:i:0 MD:Z:17A3T0C0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG +120522-2_1 16 19 121038 255 22M * 0 0 GCACTCAAACTGTGGGGGCACT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT +299969-1_1 0 19 121291 1 22M * 0 0 CGAGCGCTGCGACATTTGAGCG * HI:i:0 MD:Z:0A0A2T17 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG +67825-4_1 0 19 121291 255 22M * 0 0 AAAGTGCTGCGACATTTGAGCG * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG +90583-3_1 0 19 121291 255 22M * 0 0 AAATTGCTGCGACATTTGAGCG * MD:Z:3G18 NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG +629861-1_1 0 19 121291 1 23M * 0 0 AGAGTGCTGCGACATTTGAGCGA * HI:i:0 MD:Z:1A20T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA +120521-2_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGA * MD:Z:22T NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA +739110-1_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGT * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-372-3p|0|0|23M|23|AAAGTGCTGCGACATTTGAGCGT +270338-1_1 0 19 121291 255 23M * 0 0 AAATTGCTGCGACATTTGAGCGT * MD:Z:3G19 NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT +267649-1_1 0 19 121292 255 21M1I1M * 0 0 AAGTGCTGCGACATTTGAGCGAT * MD:Z:23 NH:i:1 NM:i:1 XN:Z:hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT +313132-1_1 0 19 121292 255 22M * 0 0 AAGTGCTGCGACATTTGAGCGT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT +270337-1_1 0 19 121292 1 4M1I18M * 0 0 AACTTGCTGCGACATTTGAGCGT * HI:i:0 MD:Z:2G19 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT +188149-2_1 0 19 122108 255 23M * 0 0 GAAGTGCTTCGATTTTGGGGTGT * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-373-3p|0|0|23M|23|GAAGTGCTTCGATTTTGGGGTGT +270393-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-498-5p|0|0|23M|23|TTTCAAGCCAGGGGGCGTTTTTC +610105-1_2 256 19 87 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA +610105-1_2 0 19 2571 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA +645839-1_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA +645839-1_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA +645839-1_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA +67830-4_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +67830-4_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +67830-4_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +535182-1_3 256 19 89 1 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +535182-1_3 0 19 89 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +535182-1_3 0 19 2573 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +766380-1_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +766380-1_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +766380-1_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +67831-4_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +67831-4_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +67831-4_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +270395-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +270395-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +270395-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +773136-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +773136-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +773136-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +102065-3_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT +102065-3_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT +102065-3_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT +37896-9_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +37896-9_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +37896-9_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +334943-1_2 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG +334943-1_2 0 19 2573 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG +270396-1_3 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT +270401-1_2 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA +270396-1_3 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT +270401-1_2 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA +270396-1_3 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT +673650-1_2 256 19 89 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT +673650-1_2 0 19 2573 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 XN:Z:hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT +150819-2_3 256 19 53 1 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +150819-2_3 0 19 53 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +150819-2_3 0 19 2537 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +270402-1_3 0 19 53 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +270402-1_3 256 19 53 1 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +270402-1_3 0 19 2537 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +752875-1_3 256 19 53 1 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +752875-1_3 0 19 53 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +752875-1_3 0 19 2537 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +369314-1_3 0 19 12413 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +369314-1_3 256 19 12413 1 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +369314-1_3 0 19 18419 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +54840-6_3 0 19 90116 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +54840-6_3 256 19 90116 1 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +54840-6_3 0 19 94508 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +423555-1_3 256 19 90117 1 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +423555-1_3 0 19 90117 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +423555-1_3 0 19 94509 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +270365-1_3 0 19 58817 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA +270365-1_3 0 19 70220 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA +270365-1_3 256 19 58817 1 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA +270366-1_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +270366-1_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +270366-1_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:3 XN:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +86082-3_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +86082-3_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +86082-3_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +270359-1_5 0 19 45641 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:1 XN:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 0 19 54440 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:2 XN:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 0 19 74691 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:4 XN:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 256 19 54440 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 XN:Z:hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 256 19 74691 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 XN:Z:hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA +752904-1_3 0 19 45646 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +752904-1_3 256 19 54445 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +752904-1_3 256 19 74696 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +105051-3_3 0 19 45646 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +105051-3_3 256 19 54445 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +105051-3_3 256 19 74696 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +120530-2_3 256 19 45681 1 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +120530-2_3 0 19 45681 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +67957-4_3 0 19 45681 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-517a-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +67957-4_3 256 19 45681 1 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-517a-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +120530-2_3 0 19 54478 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +67957-4_3 0 19 54478 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-517b-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +447402-1_1 0 19 36147 255 22M * 0 0 CAAAGCGCTCCCCTTTAGAGGT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-518b|0|0|22M|22|CAAAGCGCTCCCCTTTAGAGGT +270377-1_1 0 19 42119 255 21M * 0 0 CTCTGGAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT +751085-1_1 0 19 42119 255 20M * 0 0 CTCTGGAGGGAAGCACTTTA * MD:Z:19C NH:i:1 NM:i:1 XN:Z:hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA +270378-1_1 0 19 42119 255 22M * 0 0 CTCTGGAGGGAAGCACTTTCTG * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG +120527-2_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 68252 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 XN:Z:hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 256 19 68252 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 0 19 68252 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +531738-1_9 256 19 68252 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 XN:Z:hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 0 19 68252 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:9 XN:Z:hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +270381-1_7 256 19 68252 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:6 XN:Z:hsa-miR-518d-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 68252 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:7 XN:Z:hsa-miR-518d-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270360-1_1 0 19 63251 255 21M * 0 0 AAAGCGCTTCCCTTCAGAGTG * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-518e-3p|0|0|21M|21|AAAGCGCTTCCCTTCAGAGTG +676180-1_6 0 19 63213 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:4 XN:Z:hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 63213 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 63213 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 63213 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 63213 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 63213 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:7 XN:Z:hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +120527-2_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +95680-3_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 0 19 33390 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 0 19 33390 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +531738-1_9 0 19 33390 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:1 XN:Z:hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +347693-1_1 0 19 33390 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-518f-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTC +270348-1_3 0 19 85809 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:1 XN:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270348-1_3 0 19 95757 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:2 XN:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270348-1_3 256 19 95757 1 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270357-1_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCA * MD:Z:21T NH:i:1 NM:i:1 XN:Z:hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA +58870-5_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT +270354-1_1 0 19 85770 255 20M * 0 0 ACTCTAGAGGGAAGCGCTTT * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT +676180-1_6 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:6 XN:Z:hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 85771 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 85771 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 85771 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 85771 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 256 19 85771 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 85771 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 85771 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 85771 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:10 XN:Z:hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 85771 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 XN:Z:hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:2 XN:Z:hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 0 19 28585 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 28585 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 28585 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 28585 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 28585 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 28585 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 28585 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 28585 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:3 XN:Z:hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 28585 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 XN:Z:hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 19844 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 19844 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 19844 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 19844 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 256 19 19844 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 19844 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 256 19 19844 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 256 19 19844 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 XN:Z:hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 0 19 19844 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:2 XN:Z:hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +270371-1_1 0 19 46760 255 21M * 0 0 CAAAGTGCCTCCCTTTAGAGT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT +153079-2_1 0 19 46760 255 20M * 0 0 CAAAGTGCCTCCCTTTAGAG * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG +67829-4_1 0 19 24293 255 22M * 0 0 AAAGTGCTTCCCTTTGGACTGT * MD:Z:22 NH:i:1 NM:i:0 XN:Z:hsa-miR-520a-3p|0|0|22M|22|AAAGTGCTTCCCTTTGGACTGT +655140-1_1 0 19 24293 255 22M * 0 0 AAATTGCTTCCCTTTGGACTGT * MD:Z:3G18 NH:i:1 NM:i:1 XN:Z:hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT +485300-1_1 0 19 24293 255 23M * 0 0 AAAGTGCTTCCCTTTGGACTGTA * MD:Z:22T NH:i:1 NM:i:1 XN:Z:hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA +729311-1_1 0 19 24255 1 21M * 0 0 CTCCAGAGGGAAGTACTTTGA * HI:i:0 MD:Z:19C0T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA +720817-1_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCG * MD:Z:20T NM:i:1 NH:i:1 HI:i:1 XN:Z:hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG +120535-2_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-520a-5p|0|0|21M|21|CTCCAGAGGGAAGTACTTTCT +228043-1_1 0 19 24255 1 19M1D2M * 0 0 CTCCAGAGGGAAGTACTTTAG * HI:i:0 MD:Z:19^C0T1 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG +609803-1_1 0 19 24255 1 19M1I3M * 0 0 CTCCAGAGGGAAGTACTTTGAAG * HI:i:0 MD:Z:19C0T1 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG +101076-3_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTAGA * HI:i:0 MD:Z:19^C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA +127441-2_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTTAA * HI:i:0 MD:Z:19^C1G0T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA +103161-3_1 0 19 24255 1 20M1D2M * 0 0 CTCCAGAGGGAAGTACTTTCGA * HI:i:0 MD:Z:20^T1T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA +478794-1_1 0 19 24255 1 23M * 0 0 CTCCAGAGGGAAGTACTTTAAGA * HI:i:0 MD:Z:19C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA +744127-1_5 0 19 34626 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:2 XN:Z:hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG +744127-1_5 256 19 34626 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 XN:Z:hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG +120532-2_3 0 19 34627 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT +744127-1_5 0 19 40865 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:4 XN:Z:hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG +744127-1_5 256 19 40865 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 XN:Z:hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG +120532-2_3 256 19 40866 1 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-520c-3p|0|0|22M|22|AAAGTGCTTCCTTTTAGAGGGT +120532-2_3 0 19 40866 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-520c-3p|0|0|22M|22|AAAGTGCTTCCTTTTAGAGGGT +120527-2_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 40828 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 XN:Z:hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 256 19 40828 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +139675-2_9 0 19 40828 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +531738-1_9 256 19 40828 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 XN:Z:hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +531738-1_9 0 19 40828 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:5 XN:Z:hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +270381-1_7 256 19 40828 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:3 XN:Z:hsa-miR-520c-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 40828 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:4 XN:Z:hsa-miR-520c-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +361022-1_1 0 19 9124 255 21M * 0 0 AAAGTGCTTCCTTTTTGAGGG * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-520e-3p|0|0|21M|21|AAAGTGCTTCCTTTTTGAGGG +772976-1_1 0 19 9089 1 7M1I9M * 0 0 AAAATGGGAAGCAGTTT * HI:i:0 MD:Z:2G13 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 XN:Z:hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT +270368-1_3 0 19 55581 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 XN:Z:hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT +270369-1_1 0 19 55581 255 23M * 0 0 CAAAGTGCTTCCCTTTAGAGTGT * MD:Z:23 NH:i:1 NM:i:0 XN:Z:hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT +138559-2_2 0 19 55539 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 XN:Z:hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT +270368-1_3 0 19 75927 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 XN:Z:hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT +270368-1_3 256 19 75927 1 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 XN:Z:hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT +270358-1_1 0 19 84624 1 22M * 0 0 AGAATGGTTCCCTTTAGAGTGT * MD:Z:1A20 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 XN:Z:hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT +676180-1_6 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:5 XN:Z:hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 84586 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 84586 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 84586 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 84586 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 84586 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 84586 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 256 19 84586 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 256 19 84586 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 XN:Z:hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 0 19 84586 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:9 XN:Z:hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:3 XN:Z:hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 0 19 31760 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 31760 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 31760 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 31760 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 31760 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 31760 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 31760 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 31760 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:5 XN:Z:hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 31760 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:6 XN:Z:hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +270375-1_1 0 19 44377 255 21M * 0 0 CTACAAAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270376-1_1 0 19 44377 255 20M * 0 0 CTACAAAGGGAAGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC +57516-5_1 0 19 30907 255 20M * 0 0 CTCCAGAGGGATGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 XN:Z:hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC +102026-3_1 0 19 30907 255 21M * 0 0 CTCCAGAGGGATGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 XN:Z:hsa-miR-525-5p|0|0|21M|21|CTCCAGAGGGATGCACTTTCT +120527-2_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 39626 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA +270379-1_5 256 19 60288 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:4 XN:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA +139675-2_9 0 19 39626 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 256 19 39626 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 0 19 60288 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 256 19 60288 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +531738-1_9 0 19 39626 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:2 XN:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 256 19 39626 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 XN:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 0 19 60288 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:6 XN:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 256 19 60288 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 XN:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +270381-1_7 0 19 39626 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:1 XN:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 256 19 39626 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:2 XN:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 60288 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:5 XN:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG diff --git a/scripts/tests/files/in_aln_tag_missing_nh.sam b/scripts/tests/files/in_aln_tag_missing_nh.sam index de9326c..b8f02e2 100644 --- a/scripts/tests/files/in_aln_tag_missing_nh.sam +++ b/scripts/tests/files/in_aln_tag_missing_nh.sam @@ -4,265 +4,265 @@ @PG ID:samtools.1 PN:samtools PP:samtools VN:1.16.1 CL:samtools view -H results/test_lib/removeMultimappers.sam @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.16.1 CL:samtools view -H results/test_lib/premir_intersectedAlignments.sam @PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.16.1 CL:samtools sort -t YW -O SAM results/test_lib/mirna_intersecting_tag.sam -256497-1_1 0 19 9096 1 4M1I9M1I2M * 0 0 AAGCCAGTTTCTGTCTG * HI:i:0 MD:Z:15 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: +256497-1_1 0 19 9096 1 4M1I9M1I2M * 0 0 AAGCCAGTTTCTGTCTG * HI:i:0 MD:Z:15 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: 391978-1_2 256 19 12384 1 3M1I2M1I14M * 0 0 AAGCAACAGCACTTTCTGTAG * MD:Z:17T1 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z: 391978-1_2 0 19 18390 1 3M1I2M1I14M * 0 0 AAGCAACAGCACTTTCTGTAG * MD:Z:17T1 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z: 705321-1_1 0 19 24304 1 16M * 0 0 CTTTGGACTGTTTCTG * MD:Z:14G1 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 YW:Z: 615330-1_1 0 19 42114 1 4M1I16M * 0 0 TCACAACTCTGGAGGGAAGCA * HI:i:0 MD:Z:1G2T15 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: 623283-1_1 0 19 42116 1 2M1I16M * 0 0 ACAACTCTGGAGGGAAGCA * HI:i:0 MD:Z:2T15 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: 445515-1_1 0 19 53506 1 9M1D7M * 0 0 AAGAAAGTGTTCTCTA * HI:i:0 MD:Z:9^C6T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: -138559-2_2 256 19 75885 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z: +138559-2_2 256 19 75885 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z: 641705-1_1 0 19 121288 1 9M1I6M * 0 0 TGGAAAGTGGCTGAGA * HI:i:0 MD:Z:12C2 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z: -709268-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21 -528546-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22 -270342-1_1 0 19 121040 255 20M * 0 0 ACTCAAACTGTGGGGGCACT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-371a-5p|0|0|20M|20 -840419-1_1 0 19 121040 1 23M * 0 0 ACTCAAACTGTGGGGGCCCTTAG * HI:i:0 MD:Z:17A3T0C0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-371a-5p|0|3|23M|17A3T0C0 -120522-2_1 16 19 121038 255 22M * 0 0 GCACTCAAACTGTGGGGGCACT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-371b-3p|0|-1|22M|22 -299969-1_1 0 19 121291 1 22M * 0 0 CGAGCGCTGCGACATTTGAGCG * HI:i:0 MD:Z:0A0A2T17 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|-1|22M|0A0A2T17 -67825-4_1 0 19 121291 255 22M * 0 0 AAAGTGCTGCGACATTTGAGCG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|-1|22M|22 -90583-3_1 0 19 121291 255 22M * 0 0 AAATTGCTGCGACATTTGAGCG * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|-1|22M|3G18 -629861-1_1 0 19 121291 1 23M * 0 0 AGAGTGCTGCGACATTTGAGCGA * HI:i:0 MD:Z:1A20T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|0|23M|1A20T0 -120521-2_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|22T -739110-1_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|0|23M|23 -270338-1_1 0 19 121291 255 23M * 0 0 AAATTGCTGCGACATTTGAGCGT * MD:Z:3G19 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|3G19 -267649-1_1 0 19 121292 255 21M1I1M * 0 0 AAGTGCTGCGACATTTGAGCGAT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|1|0|21M1I1M|23 -313132-1_1 0 19 121292 255 22M * 0 0 AAGTGCTGCGACATTTGAGCGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|1|0|22M|22 -270337-1_1 0 19 121292 1 4M1I18M * 0 0 AACTTGCTGCGACATTTGAGCGT * HI:i:0 MD:Z:2G19 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|1|0|4M1I18M|2G19 -188149-2_1 0 19 122108 255 23M * 0 0 GAAGTGCTTCGATTTTGGGGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-373-3p|0|0|23M|23 -270393-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23 -610105-1_2 256 19 87 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 -610105-1_2 0 19 2571 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 -645839-1_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|20T -645839-1_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|20T -645839-1_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|20T0 -67830-4_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|21 -67830-4_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|21 -67830-4_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|21 -535182-1_3 256 19 89 1 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13 -535182-1_3 0 19 89 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13 -535182-1_3 0 19 2573 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13 -766380-1_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7 -766380-1_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7 -766380-1_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7 -67831-4_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|20 -67831-4_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|20 -67831-4_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|20 -270395-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|12A9 -270395-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|12A9 -270395-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|12A9 -773136-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|17A4 -773136-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|17A4 -773136-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|17A4 -102065-3_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|21C -102065-3_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|21C -102065-3_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|21C0 -37896-9_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|22 -37896-9_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|22 -37896-9_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|22 -334943-1_2 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0 -334943-1_2 0 19 2573 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0 -270396-1_3 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270401-1_2 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270396-1_3 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270401-1_2 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C -270396-1_3 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C0 -673650-1_2 256 19 89 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0 -673650-1_2 0 19 2573 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0 -150819-2_3 256 19 53 1 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|-1|21M|21 -150819-2_3 0 19 53 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|-1|21M|21 -150819-2_3 0 19 2537 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|-1|21M|21 -270402-1_3 0 19 53 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|-2|20M|20 -270402-1_3 256 19 53 1 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|-2|20M|20 -270402-1_3 0 19 2537 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|-2|20M|20 -752875-1_3 256 19 53 1 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-512-5p|1|0|22M|22 -752875-1_3 0 19 53 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-512-5p|1|0|22M|22 -752875-1_3 0 19 2537 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-512-5p|1|0|22M|22 -369314-1_3 0 19 12413 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-515-3p|0|-1|21M|21 -369314-1_3 256 19 12413 1 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-515-3p|0|-1|21M|21 -369314-1_3 0 19 18419 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-515-3p|0|-1|21M|21 -54840-6_3 0 19 90116 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516a-5p|0|-1|22M|22 -54840-6_3 256 19 90116 1 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516a-5p|0|-1|22M|22 -54840-6_3 0 19 94508 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516a-5p|0|-1|22M|22 -423555-1_3 256 19 90117 1 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516a-5p|1|-1|21M|21 -423555-1_3 0 19 90117 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 HI:i:2 YW:Z:hsa-miR-516a-5p|1|-1|21M|21 -423555-1_3 0 19 94509 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 HI:i:3 YW:Z:hsa-miR-516a-5p|1|-1|21M|21 -270365-1_3 0 19 58817 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C -270365-1_3 0 19 70220 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C -270365-1_3 256 19 58817 1 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C0 -270366-1_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11 -270366-1_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11 -270366-1_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11 -86082-3_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|22 -86082-3_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|22 -86082-3_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|22 -270359-1_5 0 19 45641 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 HI:i:1 YW:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 0 19 54440 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 HI:i:2 YW:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 0 19 74691 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 HI:i:4 YW:Z:hsa-miR-517-5p|-1|0|23M|22T -270359-1_5 256 19 54440 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0 -270359-1_5 256 19 74691 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0 -752904-1_3 0 19 45646 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -752904-1_3 256 19 54445 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -752904-1_3 256 19 74696 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 -105051-3_3 0 19 45646 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -105051-3_3 256 19 54445 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -105051-3_3 256 19 74696 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 -120530-2_3 256 19 45681 1 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517a-3p|0|-1|21M|21 -120530-2_3 0 19 45681 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517a-3p|0|-1|21M|21 -67957-4_3 0 19 45681 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-517a-3p|0|0|22M|22 -67957-4_3 256 19 45681 1 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-517a-3p|0|0|22M|22 -120530-2_3 0 19 54478 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517b-3p|0|-1|21M|21 -67957-4_3 0 19 54478 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-517b-3p|0|0|22M|22 -447402-1_1 0 19 36147 255 22M * 0 0 CAAAGCGCTCCCCTTTAGAGGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518b|0|0|22M|22 -270377-1_1 0 19 42119 255 21M * 0 0 CTCTGGAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|-1|21M|21 -751085-1_1 0 19 42119 255 20M * 0 0 CTCTGGAGGGAAGCACTTTA * MD:Z:19C NH:i:1 NM:i:1 YW:Z:hsa-miR-518c-5p|1|-2|20M|19C -270378-1_1 0 19 42119 255 22M * 0 0 CTCTGGAGGGAAGCACTTTCTG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|0|22M|22 -120527-2_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T -120527-2_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T0 -95680-3_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|21 -95680-3_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|21 -270379-1_5 256 19 68252 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-518d-5p|0|-1|21M|3T16T0 -139675-2_9 256 19 68252 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-2|20M|20 -139675-2_9 0 19 68252 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-2|20M|20 -531738-1_9 256 19 68252 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-3|19M|19 -531738-1_9 0 19 68252 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-3|19M|19 -270381-1_7 256 19 68252 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:6 YW:Z:hsa-miR-518d-5p|0|0|22M|22 -270381-1_7 0 19 68252 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 HI:i:7 YW:Z:hsa-miR-518d-5p|0|0|22M|22 -270360-1_1 0 19 63251 255 21M * 0 0 AAAGCGCTTCCCTTCAGAGTG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518e-3p|0|0|21M|21 -676180-1_6 0 19 63213 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:4 YW:Z:hsa-miR-518e-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 63213 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-1|21M|21 -270361-1_11 0 19 63213 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-2|20M|19C -630277-1_11 0 19 63213 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-3|19M|19 -67687-4_11 0 19 63213 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|0|22M|22 -84523-3_11 0 19 63213 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|1|23M|23 -120527-2_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|20T -95680-3_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|21 -270379-1_5 0 19 33390 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|3T16T0 -139675-2_9 0 19 33390 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-2|20M|20 -531738-1_9 0 19 33390 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-3|19M|19 -347693-1_1 0 19 33390 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518f-5p|0|0|22M|22 -270348-1_3 0 19 85809 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 HI:i:1 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270348-1_3 0 19 95757 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 NH:i:3 HI:i:2 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270348-1_3 256 19 95757 1 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18 -270357-1_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCA * MD:Z:21T NH:i:1 NM:i:1 YW:Z:hsa-miR-519a-5p|-1|-1|22M|21T -58870-5_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-1|22M|22 -270354-1_1 0 19 85770 255 20M * 0 0 ACTCTAGAGGGAAGCGCTTT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-3|20M|20 -676180-1_6 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:6 YW:Z:hsa-miR-519a-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 85771 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-1|21M|21 -18915-24_11 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-1|21M|21 -270361-1_11 0 19 85771 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C -270361-1_11 256 19 85771 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C0 -630277-1_11 0 19 85771 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-3|19M|19 -630277-1_11 256 19 85771 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-3|19M|19 -67687-4_11 256 19 85771 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|0|22M|22 -67687-4_11 0 19 85771 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|0|22M|22 -84523-3_11 0 19 85771 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|1|23M|23 -84523-3_11 256 19 85771 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|1|23M|23 -676180-1_6 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:2 YW:Z:hsa-miR-519b-5p|0|-1|21M|19C0T0 -18915-24_11 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-1|21M|21 -18915-24_11 0 19 28585 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-1|21M|21 -270361-1_11 0 19 28585 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C -270361-1_11 256 19 28585 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C0 -630277-1_11 256 19 28585 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-3|19M|19 -630277-1_11 0 19 28585 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-3|19M|19 -67687-4_11 256 19 28585 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|0|22M|22 -67687-4_11 0 19 28585 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|0|22M|22 -84523-3_11 0 19 28585 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|1|23M|23 -84523-3_11 256 19 28585 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|1|23M|23 -676180-1_6 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 19844 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|21 -18915-24_11 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-1|21M|21 -270361-1_11 0 19 19844 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C -270361-1_11 256 19 19844 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C0 -630277-1_11 0 19 19844 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-3|19M|19 -630277-1_11 256 19 19844 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-3|19M|19 -67687-4_11 0 19 19844 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|0|22M|22 -67687-4_11 256 19 19844 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|0|22M|22 -84523-3_11 256 19 19844 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-519c-5p|0|1|23M|23 -84523-3_11 0 19 19844 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|1|23M|23 -270371-1_1 0 19 46760 255 21M * 0 0 CAAAGTGCCTCCCTTTAGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-1|21M|21 -153079-2_1 0 19 46760 255 20M * 0 0 CAAAGTGCCTCCCTTTAGAG * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-2|20M|20 -67829-4_1 0 19 24293 255 22M * 0 0 AAAGTGCTTCCCTTTGGACTGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-3p|0|0|22M|22 -655140-1_1 0 19 24293 255 22M * 0 0 AAATTGCTTCCCTTTGGACTGT * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|0|22M|3G18 -485300-1_1 0 19 24293 255 23M * 0 0 AAAGTGCTTCCCTTTGGACTGTA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|1|23M|22T -729311-1_1 0 19 24255 1 21M * 0 0 CTCCAGAGGGAAGTACTTTGA * HI:i:0 MD:Z:19C0T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|0|21M|19C0T0 -720817-1_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCG * MD:Z:20T NM:i:1 NH:i:1 HI:i:1 YW:Z:hsa-miR-520a-5p|0|0|21M|20T -120535-2_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-5p|0|0|21M|21 -228043-1_1 0 19 24255 1 19M1D2M * 0 0 CTCCAGAGGGAAGTACTTTAG * HI:i:0 MD:Z:19^C0T1 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 -609803-1_1 0 19 24255 1 19M1I3M * 0 0 CTCCAGAGGGAAGTACTTTGAAG * HI:i:0 MD:Z:19C0T1 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 -101076-3_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTAGA * HI:i:0 MD:Z:19^C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 -127441-2_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTTAA * HI:i:0 MD:Z:19^C1G0T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 -103161-3_1 0 19 24255 1 20M1D2M * 0 0 CTCCAGAGGGAAGTACTTTCGA * HI:i:0 MD:Z:20^T1T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 -478794-1_1 0 19 24255 1 23M * 0 0 CTCCAGAGGGAAGTACTTTAAGA * HI:i:0 MD:Z:19C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|23M|19C0T1T0 -744127-1_5 0 19 34626 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21 -744127-1_5 256 19 34626 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21 -120532-2_3 0 19 34627 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-520b-3p|0|1|22M|22 -744127-1_5 0 19 40865 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21 -744127-1_5 256 19 40865 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21 -120532-2_3 256 19 40866 1 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520c-3p|0|0|22M|22 -120532-2_3 0 19 40866 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520c-3p|0|0|22M|22 -120527-2_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T -120527-2_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T0 -95680-3_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|21 -95680-3_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|21 -270379-1_5 256 19 40828 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520c-5p|0|-1|21M|3T16T0 -139675-2_9 256 19 40828 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-2|20M|20 -139675-2_9 0 19 40828 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-2|20M|20 -531738-1_9 256 19 40828 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-3|19M|19 -531738-1_9 0 19 40828 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-3|19M|19 -270381-1_7 256 19 40828 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:3 YW:Z:hsa-miR-520c-5p|0|0|22M|22 -270381-1_7 0 19 40828 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 HI:i:4 YW:Z:hsa-miR-520c-5p|0|0|22M|22 -361022-1_1 0 19 9124 255 21M * 0 0 AAAGTGCTTCCTTTTTGAGGG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520e-3p|0|0|21M|21 -772976-1_1 0 19 9089 1 7M1I9M * 0 0 AAAATGGGAAGCAGTTT * HI:i:0 MD:Z:2G13 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520e-5p|3|-3|7M1I9M|2G13 -270368-1_3 0 19 55581 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-520g-3p|1|-2|21M|21 -270369-1_1 0 19 55581 255 23M * 0 0 CAAAGTGCTTCCCTTTAGAGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-520g-3p|1|0|23M|23 -138559-2_2 0 19 55539 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 -270368-1_3 0 19 75927 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520h|1|0|21M|21 -270368-1_3 256 19 75927 1 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520h|1|0|21M|21 -270358-1_1 0 19 84624 1 22M * 0 0 AGAATGGTTCCCTTTAGAGTGT * MD:Z:1A20 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 YW:Z:hsa-miR-522-3p|0|0|22M|1A20 -676180-1_6 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:5 YW:Z:hsa-miR-522-5p|0|-1|21M|19C0T0 -18915-24_11 0 19 84586 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-1|21M|21 -18915-24_11 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-1|21M|21 -270361-1_11 0 19 84586 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-2|20M|19C -270361-1_11 256 19 84586 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-2|20M|19C0 -630277-1_11 256 19 84586 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-3|19M|19 -630277-1_11 0 19 84586 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-3|19M|19 -67687-4_11 0 19 84586 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|0|22M|22 -67687-4_11 256 19 84586 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|0|22M|22 -84523-3_11 256 19 84586 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|1|23M|23 -84523-3_11 0 19 84586 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|1|23M|23 -676180-1_6 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:3 YW:Z:hsa-miR-523-5p|0|-1|21M|19C0T0 -18915-24_11 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-1|21M|21 -18915-24_11 0 19 31760 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-1|21M|21 -270361-1_11 0 19 31760 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-2|20M|19C -270361-1_11 256 19 31760 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-2|20M|19C0 -630277-1_11 256 19 31760 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-3|19M|19 -630277-1_11 0 19 31760 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 HI:i:6 YW:Z:hsa-miR-523-5p|0|-3|19M|19 -67687-4_11 256 19 31760 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|0|22M|22 -67687-4_11 0 19 31760 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|0|22M|22 -84523-3_11 0 19 31760 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|1|23M|23 -84523-3_11 256 19 31760 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|1|23M|23 -270375-1_1 0 19 44377 255 21M * 0 0 CTACAAAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-1|21M|21 -270376-1_1 0 19 44377 255 20M * 0 0 CTACAAAGGGAAGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-2|20M|20 -57516-5_1 0 19 30907 255 20M * 0 0 CTCCAGAGGGATGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|-1|20M|20 -102026-3_1 0 19 30907 255 21M * 0 0 CTCCAGAGGGATGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|0|21M|21 -120527-2_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T -120527-2_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T -120527-2_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0 -120527-2_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0 -95680-3_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -95680-3_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|21 -270379-1_5 256 19 39626 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0 -270379-1_5 256 19 60288 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0 -139675-2_9 0 19 39626 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 256 19 39626 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 0 19 60288 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -139675-2_9 256 19 60288 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-2|20M|20 -531738-1_9 0 19 39626 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 256 19 39626 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 0 19 60288 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -531738-1_9 256 19 60288 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-3|19M|19 -270381-1_7 0 19 39626 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 HI:i:1 YW:Z:hsa-miR-526a-5p|0|0|22M|22 -270381-1_7 256 19 39626 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:2 YW:Z:hsa-miR-526a-5p|0|0|22M|22 -270381-1_7 0 19 60288 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 HI:i:5 YW:Z:hsa-miR-526a-5p|0|0|22M|22 +709268-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NM:i:0 YW:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC +528546-1_1 0 19 5338 255 22M * 0 0 TCAAAACTGAGGGGCATTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|22M|22|TCAAAACTGAGGGGCATTTTCT +270342-1_1 0 19 121040 255 20M * 0 0 ACTCAAACTGTGGGGGCACT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-371a-5p|0|0|20M|20|ACTCAAACTGTGGGGGCACT +840419-1_1 0 19 121040 1 23M * 0 0 ACTCAAACTGTGGGGGCCCTTAG * HI:i:0 MD:Z:17A3T0C0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG +120522-2_1 16 19 121038 255 22M * 0 0 GCACTCAAACTGTGGGGGCACT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT +299969-1_1 0 19 121291 1 22M * 0 0 CGAGCGCTGCGACATTTGAGCG * HI:i:0 MD:Z:0A0A2T17 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG +67825-4_1 0 19 121291 255 22M * 0 0 AAAGTGCTGCGACATTTGAGCG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG +90583-3_1 0 19 121291 255 22M * 0 0 AAATTGCTGCGACATTTGAGCG * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG +629861-1_1 0 19 121291 1 23M * 0 0 AGAGTGCTGCGACATTTGAGCGA * HI:i:0 MD:Z:1A20T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA +120521-2_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA +739110-1_1 0 19 121291 255 23M * 0 0 AAAGTGCTGCGACATTTGAGCGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|0|0|23M|23|AAAGTGCTGCGACATTTGAGCGT +270338-1_1 0 19 121291 255 23M * 0 0 AAATTGCTGCGACATTTGAGCGT * MD:Z:3G19 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT +267649-1_1 0 19 121292 255 21M1I1M * 0 0 AAGTGCTGCGACATTTGAGCGAT * MD:Z:23 NH:i:1 NM:i:1 YW:Z:hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT +313132-1_1 0 19 121292 255 22M * 0 0 AAGTGCTGCGACATTTGAGCGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT +270337-1_1 0 19 121292 1 4M1I18M * 0 0 AACTTGCTGCGACATTTGAGCGT * HI:i:0 MD:Z:2G19 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT +188149-2_1 0 19 122108 255 23M * 0 0 GAAGTGCTTCGATTTTGGGGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-373-3p|0|0|23M|23|GAAGTGCTTCGATTTTGGGGTGT +270393-1_1 0 19 7590 255 23M * 0 0 TTTCAAGCCAGGGGGCGTTTTTC * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-498-5p|0|0|23M|23|TTTCAAGCCAGGGGGCGTTTTTC +610105-1_2 256 19 87 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA +610105-1_2 0 19 2571 1 3M1I17M * 0 0 GAACAGTGCTGTGATAACTGA * MD:Z:11C3G4 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA +645839-1_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA +645839-1_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA +645839-1_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA +67830-4_3 256 19 89 1 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +67830-4_3 0 19 89 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +67830-4_3 0 19 2573 255 21M * 0 0 AAGTGCTGTCATAGCTGAGGT * MD:Z:21 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT +535182-1_3 256 19 89 1 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +535182-1_3 0 19 89 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 HI:i:2 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +535182-1_3 0 19 2573 255 21M * 0 0 AAGTGCTTTCATAGCTGAGGT * MD:Z:7G13 NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT +766380-1_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +766380-1_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +766380-1_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATCGCTGAGG * MD:Z:12A7 NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG +67831-4_3 0 19 89 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 HI:i:1 YW:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +67831-4_3 256 19 89 1 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +67831-4_3 0 19 2573 255 20M * 0 0 AAGTGCTGTCATAGCTGAGG * MD:Z:20 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG +270395-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +270395-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +270395-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATCGCTGAGGTC * MD:Z:12A9 NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC +773136-1_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +773136-1_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +773136-1_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGCGGTC * MD:Z:17A4 NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC +102065-3_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT +102065-3_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT +102065-3_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTT * MD:Z:21C0 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT +37896-9_3 256 19 89 1 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +37896-9_3 0 19 89 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 HI:i:2 YW:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +37896-9_3 0 19 2573 255 22M * 0 0 AAGTGCTGTCATAGCTGAGGTC * MD:Z:22 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-3p|0|0|22M|22|AAGTGCTGTCATAGCTGAGGTC +334943-1_2 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG +334943-1_2 0 19 2573 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTAG * MD:Z:21C0C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG +270396-1_3 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT +270401-1_2 0 19 89 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA +270396-1_3 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C NM:i:1 HI:i:3 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT +270401-1_2 0 19 2573 255 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCA * MD:Z:22C NM:i:1 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA +270396-1_3 256 19 89 1 23M * 0 0 AAGTGCTGTCATAGCTGAGGTCT * MD:Z:22C0 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT +673650-1_2 256 19 89 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT +673650-1_2 0 19 2573 1 23M * 0 0 AAGAGCTGTCATAGCTGAGGTCT * MD:Z:3T18C0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT +150819-2_3 256 19 53 1 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +150819-2_3 0 19 53 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 HI:i:2 YW:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +150819-2_3 0 19 2537 255 21M * 0 0 ACTCAGCCTTGAGGGCACTTT * MD:Z:21 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT +270402-1_3 0 19 53 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 HI:i:1 YW:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +270402-1_3 256 19 53 1 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +270402-1_3 0 19 2537 255 20M * 0 0 ACTCAGCCTTGAGGGCACTT * MD:Z:20 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT +752875-1_3 256 19 53 1 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +752875-1_3 0 19 53 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 HI:i:2 YW:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +752875-1_3 0 19 2537 255 22M * 0 0 ACTCAGCCTTGAGGGCACTTTC * MD:Z:22 NM:i:0 HI:i:3 YW:Z:hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC +369314-1_3 0 19 12413 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 HI:i:1 YW:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +369314-1_3 256 19 12413 1 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +369314-1_3 0 19 18419 255 21M * 0 0 GAGTGCCTTCTTTTGGAGCGT * MD:Z:21 NM:i:0 HI:i:3 YW:Z:hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT +54840-6_3 0 19 90116 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 HI:i:1 YW:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +54840-6_3 256 19 90116 1 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +54840-6_3 0 19 94508 255 22M * 0 0 TTCTCGAGGAAAGAAGCACTTT * MD:Z:22 NM:i:0 HI:i:3 YW:Z:hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT +423555-1_3 256 19 90117 1 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +423555-1_3 0 19 90117 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 HI:i:2 YW:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +423555-1_3 0 19 94509 255 21M * 0 0 TCTCGAGGAAAGAAGCACTTT * MD:Z:21 NM:i:0 HI:i:3 YW:Z:hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT +270365-1_3 0 19 58817 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 HI:i:2 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA +270365-1_3 0 19 70220 255 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C NM:i:1 HI:i:3 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA +270365-1_3 256 19 58817 1 19M * 0 0 ATCTGGAGGTAAGAAGCAA * MD:Z:18C0 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA +270366-1_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +270366-1_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +270366-1_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTCAGAAGCACTTT * MD:Z:10A11 NM:i:1 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT +86082-3_3 256 19 58817 1 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +86082-3_3 0 19 58817 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 HI:i:2 YW:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +86082-3_3 0 19 70220 255 22M * 0 0 ATCTGGAGGTAAGAAGCACTTT * MD:Z:22 NM:i:0 HI:i:3 YW:Z:hsa-miR-516b-5p|0|0|22M|22|ATCTGGAGGTAAGAAGCACTTT +270359-1_5 0 19 45641 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:1 YW:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 0 19 54440 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:2 YW:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 0 19 74691 255 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T NM:i:1 NH:i:5 HI:i:4 YW:Z:hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 256 19 54440 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA +270359-1_5 256 19 74691 1 23M * 0 0 CCCTCTAGATGGAAGCACTGTCA * MD:Z:22T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA +752904-1_3 0 19 45646 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +752904-1_3 256 19 54445 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +752904-1_3 256 19 74696 1 6M1D13M * 0 0 GAGATGAAGCACTGTCTGT * MD:Z:0T5^G13 NM:i:2 RG:Z:A1 YZ:Z:0 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT +105051-3_3 0 19 45646 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +105051-3_3 256 19 54445 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +105051-3_3 256 19 74696 1 6M1D13M * 0 0 TAGATGAAGCACTGTATGT * MD:Z:6^G9C3 NM:i:2 RG:Z:A1 YZ:Z:0 HI:i:3 YW:Z:hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT +120530-2_3 256 19 45681 1 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:1 YW:Z:hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +120530-2_3 0 19 45681 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 HI:i:2 YW:Z:hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +67957-4_3 0 19 45681 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 HI:i:1 YW:Z:hsa-miR-517a-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +67957-4_3 256 19 45681 1 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-517a-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +120530-2_3 0 19 54478 255 21M * 0 0 ATCGTGCATCCCTTTAGAGTG * MD:Z:21 NM:i:0 HI:i:3 YW:Z:hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG +67957-4_3 0 19 54478 255 22M * 0 0 ATCGTGCATCCCTTTAGAGTGT * MD:Z:22 NM:i:0 HI:i:3 YW:Z:hsa-miR-517b-3p|0|0|22M|22|ATCGTGCATCCCTTTAGAGTGT +447402-1_1 0 19 36147 255 22M * 0 0 CAAAGCGCTCCCCTTTAGAGGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518b|0|0|22M|22|CAAAGCGCTCCCCTTTAGAGGT +270377-1_1 0 19 42119 255 21M * 0 0 CTCTGGAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT +751085-1_1 0 19 42119 255 20M * 0 0 CTCTGGAGGGAAGCACTTTA * MD:Z:19C NH:i:1 NM:i:1 YW:Z:hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA +270378-1_1 0 19 42119 255 22M * 0 0 CTCTGGAGGGAAGCACTTTCTG * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG +120527-2_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 0 19 68252 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 256 19 68252 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 68252 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 256 19 68252 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 0 19 68252 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +531738-1_9 256 19 68252 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:8 YW:Z:hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 0 19 68252 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:9 YW:Z:hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +270381-1_7 256 19 68252 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:6 YW:Z:hsa-miR-518d-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 68252 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:7 YW:Z:hsa-miR-518d-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270360-1_1 0 19 63251 255 21M * 0 0 AAAGCGCTTCCCTTCAGAGTG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-518e-3p|0|0|21M|21|AAAGCGCTTCCCTTCAGAGTG +676180-1_6 0 19 63213 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:4 YW:Z:hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 63213 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 63213 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 63213 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 63213 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 63213 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:7 YW:Z:hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +120527-2_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +95680-3_9 0 19 33390 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 0 19 33390 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 0 19 33390 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +531738-1_9 0 19 33390 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:1 YW:Z:hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +347693-1_1 0 19 33390 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-518f-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTC +270348-1_3 0 19 85809 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 HI:i:1 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270348-1_3 0 19 95757 255 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 HI:i:2 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270348-1_3 256 19 95757 1 22M * 0 0 AAATTGCATCCTTTTAGAGTGT * MD:Z:3G18 NM:i:1 RG:Z:A1 YZ:Z:0 HI:i:3 YW:Z:hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT +270357-1_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCA * MD:Z:21T NH:i:1 NM:i:1 YW:Z:hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA +58870-5_1 0 19 85770 255 22M * 0 0 ACTCTAGAGGGAAGCGCTTTCT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT +270354-1_1 0 19 85770 255 20M * 0 0 ACTCTAGAGGGAAGCGCTTT * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT +676180-1_6 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:6 YW:Z:hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 85771 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 85771 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 85771 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 85771 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 85771 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 256 19 85771 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 85771 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 85771 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 85771 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:10 YW:Z:hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 85771 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:11 YW:Z:hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:2 YW:Z:hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 256 19 28585 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 0 19 28585 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 28585 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 28585 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 28585 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 28585 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 28585 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 28585 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 28585 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:3 YW:Z:hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 28585 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:4 YW:Z:hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 19844 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 19844 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 19844 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 19844 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 0 19 19844 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 256 19 19844 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 19844 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 256 19 19844 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 256 19 19844 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:1 YW:Z:hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 0 19 19844 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:2 YW:Z:hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +270371-1_1 0 19 46760 255 21M * 0 0 CAAAGTGCCTCCCTTTAGAGT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT +153079-2_1 0 19 46760 255 20M * 0 0 CAAAGTGCCTCCCTTTAGAG * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG +67829-4_1 0 19 24293 255 22M * 0 0 AAAGTGCTTCCCTTTGGACTGT * MD:Z:22 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-3p|0|0|22M|22|AAAGTGCTTCCCTTTGGACTGT +655140-1_1 0 19 24293 255 22M * 0 0 AAATTGCTTCCCTTTGGACTGT * MD:Z:3G18 NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT +485300-1_1 0 19 24293 255 23M * 0 0 AAAGTGCTTCCCTTTGGACTGTA * MD:Z:22T NH:i:1 NM:i:1 YW:Z:hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA +729311-1_1 0 19 24255 1 21M * 0 0 CTCCAGAGGGAAGTACTTTGA * HI:i:0 MD:Z:19C0T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA +720817-1_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCG * MD:Z:20T NM:i:1 NH:i:1 HI:i:1 YW:Z:hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG +120535-2_1 0 19 24255 255 21M * 0 0 CTCCAGAGGGAAGTACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520a-5p|0|0|21M|21|CTCCAGAGGGAAGTACTTTCT +228043-1_1 0 19 24255 1 19M1D2M * 0 0 CTCCAGAGGGAAGTACTTTAG * HI:i:0 MD:Z:19^C0T1 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG +609803-1_1 0 19 24255 1 19M1I3M * 0 0 CTCCAGAGGGAAGTACTTTGAAG * HI:i:0 MD:Z:19C0T1 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG +101076-3_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTAGA * HI:i:0 MD:Z:19^C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA +127441-2_1 0 19 24255 1 19M1D3M * 0 0 CTCCAGAGGGAAGTACTTTTAA * HI:i:0 MD:Z:19^C1G0T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA +103161-3_1 0 19 24255 1 20M1D2M * 0 0 CTCCAGAGGGAAGTACTTTCGA * HI:i:0 MD:Z:20^T1T0 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA +478794-1_1 0 19 24255 1 23M * 0 0 CTCCAGAGGGAAGTACTTTAAGA * HI:i:0 MD:Z:19C0T1T0 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA +744127-1_5 0 19 34626 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG +744127-1_5 256 19 34626 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG +120532-2_3 0 19 34627 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 HI:i:1 YW:Z:hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT +744127-1_5 0 19 40865 255 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG +744127-1_5 256 19 40865 1 21M * 0 0 GAAAGTGCTTCCTTTTAGAGG * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:5 YW:Z:hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG +120532-2_3 256 19 40866 1 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:2 YW:Z:hsa-miR-520c-3p|0|0|22M|22|AAAGTGCTTCCTTTTAGAGGGT +120532-2_3 0 19 40866 255 22M * 0 0 AAAGTGCTTCCTTTTAGAGGGT * MD:Z:22 NM:i:0 HI:i:3 YW:Z:hsa-miR-520c-3p|0|0|22M|22|AAAGTGCTTCCTTTTAGAGGGT +120527-2_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 256 19 40828 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 40828 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 40828 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:3 YW:Z:hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA +139675-2_9 256 19 40828 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +139675-2_9 0 19 40828 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC +531738-1_9 256 19 40828 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:4 YW:Z:hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +531738-1_9 0 19 40828 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:5 YW:Z:hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT +270381-1_7 256 19 40828 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:3 YW:Z:hsa-miR-520c-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 40828 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:4 YW:Z:hsa-miR-520c-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +361022-1_1 0 19 9124 255 21M * 0 0 AAAGTGCTTCCTTTTTGAGGG * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-520e-3p|0|0|21M|21|AAAGTGCTTCCTTTTTGAGGG +772976-1_1 0 19 9089 1 7M1I9M * 0 0 AAAATGGGAAGCAGTTT * HI:i:0 MD:Z:2G13 NH:i:1 NM:i:2 RG:Z:A1 YZ:Z:0 YW:Z:hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT +270368-1_3 0 19 55581 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 HI:i:1 YW:Z:hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT +270369-1_1 0 19 55581 255 23M * 0 0 CAAAGTGCTTCCCTTTAGAGTGT * MD:Z:23 NH:i:1 NM:i:0 YW:Z:hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT +138559-2_2 0 19 55539 1 12M1D2M1D2M1I6M * 0 0 CCCTCTAGAGGAGCCTGTTCTGT * MD:Z:12^A2^A8 NM:i:3 RG:Z:A1 YZ:Z:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT +270368-1_3 0 19 75927 255 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 HI:i:2 YW:Z:hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT +270368-1_3 256 19 75927 1 21M * 0 0 CAAAGTGCTTCCCTTTAGAGT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 HI:i:3 YW:Z:hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT +270358-1_1 0 19 84624 1 22M * 0 0 AGAATGGTTCCCTTTAGAGTGT * MD:Z:1A20 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:1 HI:i:1 YW:Z:hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT +676180-1_6 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:5 YW:Z:hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 0 19 84586 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 256 19 84586 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 84586 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 84586 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 84586 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 84586 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 0 19 84586 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 256 19 84586 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 256 19 84586 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:8 YW:Z:hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 0 19 84586 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:9 YW:Z:hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +676180-1_6 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTAA * MD:Z:19C0T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:6 HI:i:3 YW:Z:hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA +18915-24_11 256 19 31760 1 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +18915-24_11 0 19 31760 255 21M * 0 0 CTCTAGAGGGAAGCGCTTTCT * MD:Z:21 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270361-1_11 0 19 31760 255 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C NM:i:1 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA +270361-1_11 256 19 31760 1 20M * 0 0 CTCTAGAGGGAAGCGCTTTA * MD:Z:19C0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA +630277-1_11 256 19 31760 1 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +630277-1_11 0 19 31760 255 19M * 0 0 CTCTAGAGGGAAGCGCTTT * MD:Z:19 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT +67687-4_11 256 19 31760 1 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +67687-4_11 0 19 31760 255 22M * 0 0 CTCTAGAGGGAAGCGCTTTCTG * MD:Z:22 NM:i:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|0|22M|22|CTCTAGAGGGAAGCGCTTTCTG +84523-3_11 0 19 31760 255 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 NH:i:11 HI:i:5 YW:Z:hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +84523-3_11 256 19 31760 1 23M * 0 0 CTCTAGAGGGAAGCGCTTTCTGT * MD:Z:23 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:11 HI:i:6 YW:Z:hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT +270375-1_1 0 19 44377 255 21M * 0 0 CTACAAAGGGAAGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT +270376-1_1 0 19 44377 255 20M * 0 0 CTACAAAGGGAAGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC +57516-5_1 0 19 30907 255 20M * 0 0 CTCCAGAGGGATGCACTTTC * MD:Z:20 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC +102026-3_1 0 19 30907 255 21M * 0 0 CTCCAGAGGGATGCACTTTCT * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-525-5p|0|0|21M|21|CTCCAGAGGGATGCACTTTCT +120527-2_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T NM:i:1 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +120527-2_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCA * MD:Z:20T0 NM:i:1 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA +95680-3_9 256 19 39626 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 39626 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 256 19 60288 1 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +95680-3_9 0 19 60288 255 21M * 0 0 CTCTAGAGGGAAGCACTTTCT * MD:Z:21 NM:i:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT +270379-1_5 256 19 39626 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA +270379-1_5 256 19 60288 1 21M * 0 0 CTCGAGAGGGAAGCACTTTCA * MD:Z:3T16T0 NM:i:2 RG:Z:A1 YZ:Z:0 NH:i:5 HI:i:4 YW:Z:hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA +139675-2_9 0 19 39626 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 256 19 39626 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 0 19 60288 255 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +139675-2_9 256 19 60288 1 20M * 0 0 CTCTAGAGGGAAGCACTTTC * MD:Z:20 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC +531738-1_9 0 19 39626 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:2 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 256 19 39626 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:3 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 0 19 60288 255 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 NH:i:9 HI:i:6 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +531738-1_9 256 19 60288 1 19M * 0 0 CTCTAGAGGGAAGCACTTT * MD:Z:19 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:9 HI:i:7 YW:Z:hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT +270381-1_7 0 19 39626 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:1 YW:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 256 19 39626 1 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 RG:Z:A1 YZ:Z:0 NH:i:7 HI:i:2 YW:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG +270381-1_7 0 19 60288 255 22M * 0 0 CTCTAGAGGGAAGCACTTTCTG * MD:Z:22 NM:i:0 NH:i:7 HI:i:5 YW:Z:hsa-miR-526a-5p|0|0|22M|22|CTCTAGAGGGAAGCACTTTCTG diff --git a/scripts/tests/files/iso_mirna_quantification b/scripts/tests/files/iso_mirna_quantification index 634dfa9..984b6d8 100644 --- a/scripts/tests/files/iso_mirna_quantification +++ b/scripts/tests/files/iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 hsa-miR-1323 1.0 hsa-miR-371a-5p 1.0 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 -hsa-miR-371b-3p|0|-1|22M|22 2.0 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 -hsa-miR-372-3p|0|-1|22M|22 4.0 -hsa-miR-372-3p|0|-1|22M|3G18 3.0 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 -hsa-miR-372-3p|0|0|23M|22T 2.0 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 hsa-miR-372-3p 1.0 -hsa-miR-372-3p|0|0|23M|3G19 1.0 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 -hsa-miR-372-3p|1|0|22M|22 1.0 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 hsa-miR-373-3p 2.0 hsa-miR-498-5p 1.0 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 -hsa-miR-512-3p|0|-1|21M|21 4.0 -hsa-miR-512-3p|0|-1|21M|7G13 1.0 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 -hsa-miR-512-3p|0|-2|20M|20 4.0 -hsa-miR-512-3p|0|0|22M|12A9 1.0 -hsa-miR-512-3p|0|0|22M|17A4 1.0 -hsa-miR-512-3p|0|0|22M|21C 2.0 -hsa-miR-512-3p|0|0|22M|21C0 1.0 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 hsa-miR-512-3p 9.0 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 -hsa-miR-512-5p|1|-1|21M|21 2.0 -hsa-miR-512-5p|1|-2|20M|20 1.0 -hsa-miR-512-5p|1|0|22M|22 1.0 -hsa-miR-515-3p|0|-1|21M|21 1.0 -hsa-miR-516a-5p|0|-1|22M|22 6.0 -hsa-miR-516a-5p|1|-1|21M|21 1.0 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 hsa-miR-516b-5p 3.0 -hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 -hsa-miR-517a-3p|0|-1|21M|21 1.3333333333333333 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 hsa-miR-517a-3p 2.6666666666666665 -hsa-miR-517b-3p|0|-1|21M|21 0.6666666666666666 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 hsa-miR-517b-3p 1.3333333333333333 hsa-miR-518b 1.0 -hsa-miR-518c-5p|1|-1|21M|21 1.0 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 -hsa-miR-518c-5p|1|0|22M|22 1.0 -hsa-miR-518d-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-518d-5p|0|-1|21M|20T0 0.2222222222222222 -hsa-miR-518d-5p|0|-1|21M|21 0.6666666666666666 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-518d-5p|0|-2|20M|20 0.4444444444444444 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 hsa-miR-518d-5p 0.2857142857142857 hsa-miR-518e-3p 1.0 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-518e-5p|0|-1|21M|21 2.1818181818181817 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 hsa-miR-518e-5p 0.36363636363636365 -hsa-miR-518e-5p|0|1|23M|23 0.2727272727272727 -hsa-miR-518f-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-518f-5p|0|-1|21M|21 0.3333333333333333 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-518f-5p|0|-2|20M|20 0.2222222222222222 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 hsa-miR-518f-5p 1.0 -hsa-miR-519a-3p|0|0|22M|3G18 1.0 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 -hsa-miR-519a-5p|-1|-1|22M|22 5.0 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519a-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-519a-5p 0.7272727272727273 -hsa-miR-519a-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519b-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519b-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-519b-5p 0.7272727272727273 -hsa-miR-519b-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519c-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-519c-5p 0.7272727272727273 -hsa-miR-519c-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519d-3p|0|-1|21M|21 1.0 -hsa-miR-519d-3p|0|-2|20M|20 2.0 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 hsa-miR-520a-3p 4.0 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 -hsa-miR-520a-3p|0|1|23M|22T 1.0 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 -hsa-miR-520a-5p|0|0|21M|20T 1.0 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 hsa-miR-520a-5p 2.0 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 3.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 2.0 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 3.0 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 -hsa-miR-520b-3p|0|1|22M|22 0.6666666666666666 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 hsa-miR-520c-3p 1.3333333333333333 -hsa-miR-520c-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-520c-5p|0|-1|21M|20T0 0.2222222222222222 -hsa-miR-520c-5p|0|-1|21M|21 0.6666666666666666 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-520c-5p|0|-2|20M|20 0.4444444444444444 -hsa-miR-520c-5p|0|-3|19M|19 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 hsa-miR-520c-5p 0.2857142857142857 hsa-miR-520e-3p 1.0 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 -hsa-miR-520g-3p|1|0|23M|23 1.0 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 -hsa-miR-522-3p|0|0|22M|1A20 1.0 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-522-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-522-5p 0.7272727272727273 -hsa-miR-522-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-523-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-523-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-523-5p 0.7272727272727273 -hsa-miR-523-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-524-5p|0|-1|21M|21 1.0 -hsa-miR-524-5p|0|-2|20M|20 1.0 -hsa-miR-525-5p|0|-1|20M|20 5.0 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 hsa-miR-525-5p 3.0 -hsa-miR-526a-5p|0|-1|21M|20T 0.4444444444444444 -hsa-miR-526a-5p|0|-1|21M|20T0 0.4444444444444444 -hsa-miR-526a-5p|0|-1|21M|21 1.3333333333333333 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 -hsa-miR-526a-5p|0|-2|20M|20 0.8888888888888888 -hsa-miR-526a-5p|0|-3|19M|19 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 hsa-miR-526a-5p 0.42857142857142855 diff --git a/scripts/tests/files/iso_quantification b/scripts/tests/files/iso_quantification index 9e5cdd7..2906ac7 100644 --- a/scripts/tests/files/iso_quantification +++ b/scripts/tests/files/iso_quantification @@ -1,131 +1,134 @@ -hsa-miR-1323|0|-1|21M|21 1.0 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 -hsa-miR-371b-3p|0|-1|22M|22 2.0 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 -hsa-miR-372-3p|0|-1|22M|22 4.0 -hsa-miR-372-3p|0|-1|22M|3G18 3.0 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 -hsa-miR-372-3p|0|0|23M|22T 2.0 -hsa-miR-372-3p|0|0|23M|3G19 1.0 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 -hsa-miR-372-3p|1|0|22M|22 1.0 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 -hsa-miR-512-3p|0|-1|21M|21 4.0 -hsa-miR-512-3p|0|-1|21M|7G13 1.0 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 -hsa-miR-512-3p|0|-2|20M|20 4.0 -hsa-miR-512-3p|0|0|22M|12A9 1.0 -hsa-miR-512-3p|0|0|22M|17A4 1.0 -hsa-miR-512-3p|0|0|22M|21C 2.0 -hsa-miR-512-3p|0|0|22M|21C0 1.0 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 -hsa-miR-512-5p|1|-1|21M|21 2.0 -hsa-miR-512-5p|1|-2|20M|20 1.0 -hsa-miR-512-5p|1|0|22M|22 1.0 -hsa-miR-515-3p|0|-1|21M|21 1.0 -hsa-miR-516a-5p|0|-1|22M|22 6.0 -hsa-miR-516a-5p|1|-1|21M|21 1.0 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 -hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 -hsa-miR-517a-3p|0|-1|21M|21 1.3333333333333333 -hsa-miR-517b-3p|0|-1|21M|21 0.6666666666666666 -hsa-miR-518c-5p|1|-1|21M|21 1.0 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 -hsa-miR-518c-5p|1|0|22M|22 1.0 -hsa-miR-518d-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-518d-5p|0|-1|21M|20T0 0.2222222222222222 -hsa-miR-518d-5p|0|-1|21M|21 0.6666666666666666 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-518d-5p|0|-2|20M|20 0.4444444444444444 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-518e-5p|0|-1|21M|21 2.1818181818181817 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 -hsa-miR-518e-5p|0|1|23M|23 0.2727272727272727 -hsa-miR-518f-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-518f-5p|0|-1|21M|21 0.3333333333333333 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-518f-5p|0|-2|20M|20 0.2222222222222222 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 -hsa-miR-519a-3p|0|0|22M|3G18 1.0 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 -hsa-miR-519a-5p|-1|-1|22M|22 5.0 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519a-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 -hsa-miR-519a-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519b-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519b-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 -hsa-miR-519b-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519c-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 -hsa-miR-519c-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519d-3p|0|-1|21M|21 1.0 -hsa-miR-519d-3p|0|-2|20M|20 2.0 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 -hsa-miR-520a-3p|0|1|23M|22T 1.0 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 -hsa-miR-520a-5p|0|0|21M|20T 1.0 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 3.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 2.0 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 3.0 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 -hsa-miR-520b-3p|0|1|22M|22 0.6666666666666666 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 -hsa-miR-520c-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-520c-5p|0|-1|21M|20T0 0.2222222222222222 -hsa-miR-520c-5p|0|-1|21M|21 0.6666666666666666 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-520c-5p|0|-2|20M|20 0.4444444444444444 -hsa-miR-520c-5p|0|-3|19M|19 0.2222222222222222 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 -hsa-miR-520g-3p|1|0|23M|23 1.0 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 -hsa-miR-522-3p|0|0|22M|1A20 1.0 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-522-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 -hsa-miR-522-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-523-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-523-5p|0|-3|19M|19 0.18181818181818182 -hsa-miR-523-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-524-5p|0|-1|21M|21 1.0 -hsa-miR-524-5p|0|-2|20M|20 1.0 -hsa-miR-525-5p|0|-1|20M|20 5.0 -hsa-miR-526a-5p|0|-1|21M|20T 0.4444444444444444 -hsa-miR-526a-5p|0|-1|21M|20T0 0.4444444444444444 -hsa-miR-526a-5p|0|-1|21M|21 1.3333333333333333 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 -hsa-miR-526a-5p|0|-2|20M|20 0.8888888888888888 -hsa-miR-526a-5p|0|-3|19M|19 0.4444444444444444 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 diff --git a/scripts/tests/files/len_ids_iso_mirna_quantification b/scripts/tests/files/len_ids_iso_mirna_quantification index 7bc2995..2080601 100644 --- a/scripts/tests/files/len_ids_iso_mirna_quantification +++ b/scripts/tests/files/len_ids_iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 22 709268-1_1 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 22 709268-1_1 hsa-miR-1323 1.0 20 528546-1_1 hsa-miR-371a-5p 1.0 23 270342-1_1 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 22 840419-1_1 -hsa-miR-371b-3p|0|-1|22M|22 2.0 22 120522-2_1 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 22 299969-1_1 -hsa-miR-372-3p|0|-1|22M|22 4.0 22 67825-4_1 -hsa-miR-372-3p|0|-1|22M|3G18 3.0 23 90583-3_1 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 23 629861-1_1 -hsa-miR-372-3p|0|0|23M|22T 2.0 23 120521-2_1 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 22 840419-1_1 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 22 120522-2_1 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 22 299969-1_1 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 22 67825-4_1 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 23 90583-3_1 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 23 629861-1_1 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 23 120521-2_1 hsa-miR-372-3p 1.0 23 739110-1_1 -hsa-miR-372-3p|0|0|23M|3G19 1.0 23 270338-1_1 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 22 267649-1_1 -hsa-miR-372-3p|1|0|22M|22 1.0 23 313132-1_1 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 23 270337-1_1 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 23 270338-1_1 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 22 267649-1_1 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 23 313132-1_1 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 23 270337-1_1 hsa-miR-373-3p 2.0 23 188149-2_1 hsa-miR-498-5p 1.0 21 270393-1_1 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 21 610105-1_2;610105-1_2 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 21 645839-1_3;645839-1_3 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 21 645839-1_3 -hsa-miR-512-3p|0|-1|21M|21 4.0 21 67830-4_3;67830-4_3;67830-4_3 -hsa-miR-512-3p|0|-1|21M|7G13 1.0 20 535182-1_3;535182-1_3;535182-1_3 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 20 766380-1_3;766380-1_3;766380-1_3 -hsa-miR-512-3p|0|-2|20M|20 4.0 22 67831-4_3;67831-4_3;67831-4_3 -hsa-miR-512-3p|0|0|22M|12A9 1.0 22 270395-1_3;270395-1_3;270395-1_3 -hsa-miR-512-3p|0|0|22M|17A4 1.0 22 773136-1_3;773136-1_3;773136-1_3 -hsa-miR-512-3p|0|0|22M|21C 2.0 22 102065-3_3;102065-3_3 -hsa-miR-512-3p|0|0|22M|21C0 1.0 22 102065-3_3 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 21 610105-1_2;610105-1_2 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 21 645839-1_3;645839-1_3 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 21 645839-1_3 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 21 67830-4_3;67830-4_3;67830-4_3 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 20 535182-1_3;535182-1_3;535182-1_3 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 20 766380-1_3;766380-1_3;766380-1_3 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 22 67831-4_3;67831-4_3;67831-4_3 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 22 270395-1_3;270395-1_3;270395-1_3 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 22 773136-1_3;773136-1_3;773136-1_3 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 22 102065-3_3;102065-3_3 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 22 102065-3_3 hsa-miR-512-3p 9.0 23 37896-9_3;37896-9_3;37896-9_3 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 23 334943-1_2;334943-1_2 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 23 270396-1_3;270401-1_2;270396-1_3;270401-1_2 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 23 270396-1_3 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 21 673650-1_2;673650-1_2 -hsa-miR-512-5p|1|-1|21M|21 2.0 20 150819-2_3;150819-2_3;150819-2_3 -hsa-miR-512-5p|1|-2|20M|20 1.0 22 270402-1_3;270402-1_3;270402-1_3 -hsa-miR-512-5p|1|0|22M|22 1.0 21 752875-1_3;752875-1_3;752875-1_3 -hsa-miR-515-3p|0|-1|21M|21 1.0 22 369314-1_3;369314-1_3;369314-1_3 -hsa-miR-516a-5p|0|-1|22M|22 6.0 21 54840-6_3;54840-6_3;54840-6_3 -hsa-miR-516a-5p|1|-1|21M|21 1.0 19 423555-1_3;423555-1_3;423555-1_3 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 19 270365-1_3;270365-1_3 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 22 270365-1_3 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 22 270366-1_3;270366-1_3;270366-1_3 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 23 334943-1_2;334943-1_2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 23 270396-1_3 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 23 270401-1_2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 23 270396-1_3 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 23 270401-1_2 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 23 270396-1_3 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 21 673650-1_2;673650-1_2 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 20 150819-2_3;150819-2_3;150819-2_3 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 22 270402-1_3;270402-1_3;270402-1_3 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 21 752875-1_3;752875-1_3;752875-1_3 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 22 369314-1_3;369314-1_3;369314-1_3 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 21 54840-6_3;54840-6_3;54840-6_3 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 19 423555-1_3;423555-1_3;423555-1_3 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 19 270365-1_3;270365-1_3 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 22 270365-1_3 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 22 270366-1_3;270366-1_3;270366-1_3 hsa-miR-516b-5p 3.0 23 86082-3_3;86082-3_3;86082-3_3 -hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 23 270359-1_5;270359-1_5;270359-1_5 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 19 270359-1_5;270359-1_5 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 19 752904-1_3;752904-1_3;752904-1_3 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 21 105051-3_3;105051-3_3;105051-3_3 -hsa-miR-517a-3p|0|-1|21M|21 1.3333333333333333 22 120530-2_3;120530-2_3 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 23 270359-1_5;270359-1_5;270359-1_5 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 19 270359-1_5;270359-1_5 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 19 752904-1_3;752904-1_3;752904-1_3 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 21 105051-3_3;105051-3_3;105051-3_3 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 22 120530-2_3;120530-2_3 hsa-miR-517a-3p 2.6666666666666665 21 67957-4_3;67957-4_3 -hsa-miR-517b-3p|0|-1|21M|21 0.6666666666666666 22 120530-2_3 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 22 120530-2_3 hsa-miR-517b-3p 1.3333333333333333 22 67957-4_3 hsa-miR-518b 1.0 21 447402-1_1 -hsa-miR-518c-5p|1|-1|21M|21 1.0 20 270377-1_1 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 22 751085-1_1 -hsa-miR-518c-5p|1|0|22M|22 1.0 21 270378-1_1 -hsa-miR-518d-5p|0|-1|21M|20T 0.2222222222222222 21 120527-2_9 -hsa-miR-518d-5p|0|-1|21M|20T0 0.2222222222222222 21 120527-2_9 -hsa-miR-518d-5p|0|-1|21M|21 0.6666666666666666 21 95680-3_9;95680-3_9 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 20 270379-1_5 -hsa-miR-518d-5p|0|-2|20M|20 0.4444444444444444 19 139675-2_9;139675-2_9 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 22 531738-1_9;531738-1_9 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 20 270377-1_1 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 22 751085-1_1 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 21 270378-1_1 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 120527-2_9 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 120527-2_9 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 21 95680-3_9;95680-3_9 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 20 270379-1_5 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 19 139675-2_9;139675-2_9 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 22 531738-1_9;531738-1_9 hsa-miR-518d-5p 0.2857142857142857 21 270381-1_7;270381-1_7 hsa-miR-518e-3p 1.0 21 270360-1_1 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 21 676180-1_6 -hsa-miR-518e-5p|0|-1|21M|21 2.1818181818181817 20 18915-24_11 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 19 270361-1_11 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 22 630277-1_11 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 676180-1_6 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 20 18915-24_11 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 270361-1_11 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 22 630277-1_11 hsa-miR-518e-5p 0.36363636363636365 23 67687-4_11 -hsa-miR-518e-5p|0|1|23M|23 0.2727272727272727 21 84523-3_11 -hsa-miR-518f-5p|0|-1|21M|20T 0.2222222222222222 21 120527-2_9 -hsa-miR-518f-5p|0|-1|21M|21 0.3333333333333333 21 95680-3_9 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 20 270379-1_5 -hsa-miR-518f-5p|0|-2|20M|20 0.2222222222222222 19 139675-2_9 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 22 531738-1_9 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 21 84523-3_11 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 120527-2_9 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 21 95680-3_9 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 20 270379-1_5 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 19 139675-2_9 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 22 531738-1_9 hsa-miR-518f-5p 1.0 22 347693-1_1 -hsa-miR-519a-3p|0|0|22M|3G18 1.0 22 270348-1_3;270348-1_3;270348-1_3 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 22 270357-1_1 -hsa-miR-519a-5p|-1|-1|22M|22 5.0 20 58870-5_1 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 21 270354-1_1 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 21 676180-1_6 -hsa-miR-519a-5p|0|-1|21M|21 4.363636363636363 20 18915-24_11;18915-24_11 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 20 270361-1_11 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 19 270361-1_11 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 22 630277-1_11;630277-1_11 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 22 270348-1_3;270348-1_3;270348-1_3 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 22 270357-1_1 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 20 58870-5_1 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 21 270354-1_1 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 676180-1_6 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 18915-24_11;18915-24_11 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 270361-1_11 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 270361-1_11 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 630277-1_11;630277-1_11 hsa-miR-519a-5p 0.7272727272727273 23 67687-4_11;67687-4_11 -hsa-miR-519a-5p|0|1|23M|23 0.5454545454545454 21 84523-3_11;84523-3_11 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 21 676180-1_6 -hsa-miR-519b-5p|0|-1|21M|21 4.363636363636363 20 18915-24_11;18915-24_11 -hsa-miR-519b-5p|0|-2|20M|19C 0.09090909090909091 20 270361-1_11 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 19 270361-1_11 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 22 630277-1_11;630277-1_11 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 84523-3_11;84523-3_11 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 676180-1_6 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 18915-24_11;18915-24_11 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 270361-1_11 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 270361-1_11 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 630277-1_11;630277-1_11 hsa-miR-519b-5p 0.7272727272727273 23 67687-4_11;67687-4_11 -hsa-miR-519b-5p|0|1|23M|23 0.5454545454545454 21 84523-3_11;84523-3_11 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 21 676180-1_6 -hsa-miR-519c-5p|0|-1|21M|21 4.363636363636363 20 18915-24_11;18915-24_11 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 20 270361-1_11 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 19 270361-1_11 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 22 630277-1_11;630277-1_11 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 84523-3_11;84523-3_11 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 676180-1_6 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 18915-24_11;18915-24_11 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 270361-1_11 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 270361-1_11 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 630277-1_11;630277-1_11 hsa-miR-519c-5p 0.7272727272727273 23 67687-4_11;67687-4_11 -hsa-miR-519c-5p|0|1|23M|23 0.5454545454545454 21 84523-3_11;84523-3_11 -hsa-miR-519d-3p|0|-1|21M|21 1.0 20 270371-1_1 -hsa-miR-519d-3p|0|-2|20M|20 2.0 22 153079-2_1 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 84523-3_11;84523-3_11 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 20 270371-1_1 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 22 153079-2_1 hsa-miR-520a-3p 4.0 22 67829-4_1 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 23 655140-1_1 -hsa-miR-520a-3p|0|1|23M|22T 1.0 21 485300-1_1 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 21 729311-1_1 -hsa-miR-520a-5p|0|0|21M|20T 1.0 21 720817-1_1 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 23 655140-1_1 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 21 485300-1_1 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 21 729311-1_1 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 21 720817-1_1 hsa-miR-520a-5p 2.0 21 120535-2_1 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 23 228043-1_1 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 22 609803-1_1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 3.0 22 101076-3_1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 2.0 22 127441-2_1 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 3.0 23 103161-3_1 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 21 478794-1_1 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 22 744127-1_5;744127-1_5 -hsa-miR-520b-3p|0|1|22M|22 0.6666666666666666 21 120532-2_3 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 22 744127-1_5;744127-1_5 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 23 228043-1_1 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 22 609803-1_1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 22 101076-3_1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 22 127441-2_1 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 23 103161-3_1 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 21 478794-1_1 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 22 744127-1_5;744127-1_5 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 21 120532-2_3 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 22 744127-1_5;744127-1_5 hsa-miR-520c-3p 1.3333333333333333 21 120532-2_3;120532-2_3 -hsa-miR-520c-5p|0|-1|21M|20T 0.2222222222222222 21 120527-2_9 -hsa-miR-520c-5p|0|-1|21M|20T0 0.2222222222222222 21 120527-2_9 -hsa-miR-520c-5p|0|-1|21M|21 0.6666666666666666 21 95680-3_9;95680-3_9 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 20 270379-1_5 -hsa-miR-520c-5p|0|-2|20M|20 0.4444444444444444 19 139675-2_9;139675-2_9 -hsa-miR-520c-5p|0|-3|19M|19 0.2222222222222222 22 531738-1_9;531738-1_9 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 120527-2_9 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 120527-2_9 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 21 95680-3_9;95680-3_9 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 20 270379-1_5 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 19 139675-2_9;139675-2_9 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 22 531738-1_9;531738-1_9 hsa-miR-520c-5p 0.2857142857142857 21 270381-1_7;270381-1_7 hsa-miR-520e-3p 1.0 17 361022-1_1 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 21 772976-1_1 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 23 270368-1_3 -hsa-miR-520g-3p|1|0|23M|23 1.0 23 270369-1_1 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 21 138559-2_2 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 22 270368-1_3;270368-1_3 -hsa-miR-522-3p|0|0|22M|1A20 1.0 21 270358-1_1 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 21 676180-1_6 -hsa-miR-522-5p|0|-1|21M|21 4.363636363636363 20 18915-24_11;18915-24_11 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 20 270361-1_11 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 19 270361-1_11 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 22 630277-1_11;630277-1_11 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 21 772976-1_1 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 23 270368-1_3 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 23 270369-1_1 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 21 138559-2_2 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 22 270368-1_3;270368-1_3 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 21 270358-1_1 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 676180-1_6 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 18915-24_11;18915-24_11 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 270361-1_11 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 270361-1_11 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 630277-1_11;630277-1_11 hsa-miR-522-5p 0.7272727272727273 23 67687-4_11;67687-4_11 -hsa-miR-522-5p|0|1|23M|23 0.5454545454545454 21 84523-3_11;84523-3_11 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 21 676180-1_6 -hsa-miR-523-5p|0|-1|21M|21 4.363636363636363 20 18915-24_11;18915-24_11 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 20 270361-1_11 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 19 270361-1_11 -hsa-miR-523-5p|0|-3|19M|19 0.18181818181818182 22 630277-1_11;630277-1_11 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 84523-3_11;84523-3_11 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 676180-1_6 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 18915-24_11;18915-24_11 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 270361-1_11 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 270361-1_11 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 630277-1_11;630277-1_11 hsa-miR-523-5p 0.7272727272727273 23 67687-4_11;67687-4_11 -hsa-miR-523-5p|0|1|23M|23 0.5454545454545454 21 84523-3_11;84523-3_11 -hsa-miR-524-5p|0|-1|21M|21 1.0 20 270375-1_1 -hsa-miR-524-5p|0|-2|20M|20 1.0 20 270376-1_1 -hsa-miR-525-5p|0|-1|20M|20 5.0 21 57516-5_1 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 84523-3_11;84523-3_11 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 20 270375-1_1 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 20 270376-1_1 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 21 57516-5_1 hsa-miR-525-5p 3.0 21 102026-3_1 -hsa-miR-526a-5p|0|-1|21M|20T 0.4444444444444444 21 120527-2_9;120527-2_9 -hsa-miR-526a-5p|0|-1|21M|20T0 0.4444444444444444 21 120527-2_9;120527-2_9 -hsa-miR-526a-5p|0|-1|21M|21 1.3333333333333333 21 95680-3_9;95680-3_9;95680-3_9;95680-3_9 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 20 270379-1_5;270379-1_5 -hsa-miR-526a-5p|0|-2|20M|20 0.8888888888888888 19 139675-2_9;139675-2_9;139675-2_9;139675-2_9 -hsa-miR-526a-5p|0|-3|19M|19 0.4444444444444444 22 531738-1_9;531738-1_9;531738-1_9;531738-1_9 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 21 120527-2_9;120527-2_9 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 21 120527-2_9;120527-2_9 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 21 95680-3_9;95680-3_9;95680-3_9;95680-3_9 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 20 270379-1_5;270379-1_5 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 19 139675-2_9;139675-2_9;139675-2_9;139675-2_9 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 22 531738-1_9;531738-1_9;531738-1_9;531738-1_9 hsa-miR-526a-5p 0.42857142857142855 22 270381-1_7;270381-1_7;270381-1_7 diff --git a/scripts/tests/files/len_iso_mirna_quantification b/scripts/tests/files/len_iso_mirna_quantification index 42c7d17..53afa18 100644 --- a/scripts/tests/files/len_iso_mirna_quantification +++ b/scripts/tests/files/len_iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 22 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 22 hsa-miR-1323 1.0 20 hsa-miR-371a-5p 1.0 23 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 22 -hsa-miR-371b-3p|0|-1|22M|22 2.0 22 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 22 -hsa-miR-372-3p|0|-1|22M|22 4.0 22 -hsa-miR-372-3p|0|-1|22M|3G18 3.0 23 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 23 -hsa-miR-372-3p|0|0|23M|22T 2.0 23 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 22 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 22 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 22 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 22 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 23 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 23 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 23 hsa-miR-372-3p 1.0 23 -hsa-miR-372-3p|0|0|23M|3G19 1.0 23 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 22 -hsa-miR-372-3p|1|0|22M|22 1.0 23 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 23 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 23 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 22 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 23 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 23 hsa-miR-373-3p 2.0 23 hsa-miR-498-5p 1.0 21 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 21 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 21 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 21 -hsa-miR-512-3p|0|-1|21M|21 4.0 21 -hsa-miR-512-3p|0|-1|21M|7G13 1.0 20 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 20 -hsa-miR-512-3p|0|-2|20M|20 4.0 22 -hsa-miR-512-3p|0|0|22M|12A9 1.0 22 -hsa-miR-512-3p|0|0|22M|17A4 1.0 22 -hsa-miR-512-3p|0|0|22M|21C 2.0 22 -hsa-miR-512-3p|0|0|22M|21C0 1.0 22 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 21 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 21 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 21 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 21 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 20 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 20 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 22 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 22 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 22 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 22 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 22 hsa-miR-512-3p 9.0 23 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 23 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 23 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 23 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 21 -hsa-miR-512-5p|1|-1|21M|21 2.0 20 -hsa-miR-512-5p|1|-2|20M|20 1.0 22 -hsa-miR-512-5p|1|0|22M|22 1.0 21 -hsa-miR-515-3p|0|-1|21M|21 1.0 22 -hsa-miR-516a-5p|0|-1|22M|22 6.0 21 -hsa-miR-516a-5p|1|-1|21M|21 1.0 19 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 19 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 22 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 22 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 23 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 23 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 23 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 23 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 23 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 23 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 21 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 20 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 22 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 21 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 22 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 21 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 19 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 19 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 22 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 22 hsa-miR-516b-5p 3.0 23 -hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 23 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 19 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 19 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 21 -hsa-miR-517a-3p|0|-1|21M|21 1.3333333333333333 22 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 23 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 19 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 19 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 21 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 22 hsa-miR-517a-3p 2.6666666666666665 21 -hsa-miR-517b-3p|0|-1|21M|21 0.6666666666666666 22 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 22 hsa-miR-517b-3p 1.3333333333333333 22 hsa-miR-518b 1.0 21 -hsa-miR-518c-5p|1|-1|21M|21 1.0 20 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 22 -hsa-miR-518c-5p|1|0|22M|22 1.0 21 -hsa-miR-518d-5p|0|-1|21M|20T 0.2222222222222222 21 -hsa-miR-518d-5p|0|-1|21M|20T0 0.2222222222222222 21 -hsa-miR-518d-5p|0|-1|21M|21 0.6666666666666666 21 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 20 -hsa-miR-518d-5p|0|-2|20M|20 0.4444444444444444 19 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 22 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 20 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 22 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 21 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 21 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 20 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 19 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 22 hsa-miR-518d-5p 0.2857142857142857 21 hsa-miR-518e-3p 1.0 21 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 21 -hsa-miR-518e-5p|0|-1|21M|21 2.1818181818181817 20 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 19 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 22 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 20 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 22 hsa-miR-518e-5p 0.36363636363636365 23 -hsa-miR-518e-5p|0|1|23M|23 0.2727272727272727 21 -hsa-miR-518f-5p|0|-1|21M|20T 0.2222222222222222 21 -hsa-miR-518f-5p|0|-1|21M|21 0.3333333333333333 21 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 20 -hsa-miR-518f-5p|0|-2|20M|20 0.2222222222222222 19 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 22 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 21 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 21 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 20 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 19 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 22 hsa-miR-518f-5p 1.0 22 -hsa-miR-519a-3p|0|0|22M|3G18 1.0 22 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 22 -hsa-miR-519a-5p|-1|-1|22M|22 5.0 20 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 21 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 21 -hsa-miR-519a-5p|0|-1|21M|21 4.363636363636363 20 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 20 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 19 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 22 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 22 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 22 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 20 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 21 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 hsa-miR-519a-5p 0.7272727272727273 23 -hsa-miR-519a-5p|0|1|23M|23 0.5454545454545454 21 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 21 -hsa-miR-519b-5p|0|-1|21M|21 4.363636363636363 20 -hsa-miR-519b-5p|0|-2|20M|19C 0.09090909090909091 20 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 19 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 22 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 hsa-miR-519b-5p 0.7272727272727273 23 -hsa-miR-519b-5p|0|1|23M|23 0.5454545454545454 21 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 21 -hsa-miR-519c-5p|0|-1|21M|21 4.363636363636363 20 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 20 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 19 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 22 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 hsa-miR-519c-5p 0.7272727272727273 23 -hsa-miR-519c-5p|0|1|23M|23 0.5454545454545454 21 -hsa-miR-519d-3p|0|-1|21M|21 1.0 20 -hsa-miR-519d-3p|0|-2|20M|20 2.0 22 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 20 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 22 hsa-miR-520a-3p 4.0 22 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 23 -hsa-miR-520a-3p|0|1|23M|22T 1.0 21 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 21 -hsa-miR-520a-5p|0|0|21M|20T 1.0 21 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 23 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 21 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 21 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 21 hsa-miR-520a-5p 2.0 21 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 23 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 22 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 3.0 22 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 2.0 22 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 3.0 23 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 21 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 22 -hsa-miR-520b-3p|0|1|22M|22 0.6666666666666666 21 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 22 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 23 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 22 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 22 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 22 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 23 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 21 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 22 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 21 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 22 hsa-miR-520c-3p 1.3333333333333333 21 -hsa-miR-520c-5p|0|-1|21M|20T 0.2222222222222222 21 -hsa-miR-520c-5p|0|-1|21M|20T0 0.2222222222222222 21 -hsa-miR-520c-5p|0|-1|21M|21 0.6666666666666666 21 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 20 -hsa-miR-520c-5p|0|-2|20M|20 0.4444444444444444 19 -hsa-miR-520c-5p|0|-3|19M|19 0.2222222222222222 22 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 21 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 21 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 20 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 19 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 22 hsa-miR-520c-5p 0.2857142857142857 21 hsa-miR-520e-3p 1.0 17 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 21 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 23 -hsa-miR-520g-3p|1|0|23M|23 1.0 23 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 21 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 22 -hsa-miR-522-3p|0|0|22M|1A20 1.0 21 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 21 -hsa-miR-522-5p|0|-1|21M|21 4.363636363636363 20 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 20 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 19 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 22 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 21 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 23 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 23 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 21 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 22 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 21 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 hsa-miR-522-5p 0.7272727272727273 23 -hsa-miR-522-5p|0|1|23M|23 0.5454545454545454 21 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 21 -hsa-miR-523-5p|0|-1|21M|21 4.363636363636363 20 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 20 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 19 -hsa-miR-523-5p|0|-3|19M|19 0.18181818181818182 22 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 21 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 20 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 20 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 19 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 22 hsa-miR-523-5p 0.7272727272727273 23 -hsa-miR-523-5p|0|1|23M|23 0.5454545454545454 21 -hsa-miR-524-5p|0|-1|21M|21 1.0 20 -hsa-miR-524-5p|0|-2|20M|20 1.0 20 -hsa-miR-525-5p|0|-1|20M|20 5.0 21 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 21 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 20 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 20 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 21 hsa-miR-525-5p 3.0 21 -hsa-miR-526a-5p|0|-1|21M|20T 0.4444444444444444 21 -hsa-miR-526a-5p|0|-1|21M|20T0 0.4444444444444444 21 -hsa-miR-526a-5p|0|-1|21M|21 1.3333333333333333 21 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 20 -hsa-miR-526a-5p|0|-2|20M|20 0.8888888888888888 19 -hsa-miR-526a-5p|0|-3|19M|19 0.4444444444444444 22 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 21 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 21 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 21 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 20 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 19 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 22 hsa-miR-526a-5p 0.42857142857142855 22 diff --git a/scripts/tests/files/missing_nh_iso_mirna_quantification b/scripts/tests/files/missing_nh_iso_mirna_quantification index 864d18a..182d1c6 100644 --- a/scripts/tests/files/missing_nh_iso_mirna_quantification +++ b/scripts/tests/files/missing_nh_iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 hsa-miR-1323 1.0 hsa-miR-371a-5p 1.0 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 -hsa-miR-371b-3p|0|-1|22M|22 1.0 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 -hsa-miR-372-3p|0|-1|22M|22 1.0 -hsa-miR-372-3p|0|-1|22M|3G18 1.0 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 -hsa-miR-372-3p|0|0|23M|22T 1.0 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 1.0 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 1.0 hsa-miR-372-3p 1.0 -hsa-miR-372-3p|0|0|23M|3G19 1.0 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 -hsa-miR-372-3p|1|0|22M|22 1.0 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 hsa-miR-373-3p 1.0 hsa-miR-498-5p 1.0 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 2.0 -hsa-miR-512-3p|0|-1|21M|20T 2.0 -hsa-miR-512-3p|0|-1|21M|20T0 1.0 -hsa-miR-512-3p|0|-1|21M|21 3.0 -hsa-miR-512-3p|0|-1|21M|7G13 5.0 -hsa-miR-512-3p|0|-2|20M|12A7 3.0 -hsa-miR-512-3p|0|-2|20M|20 5.0 -hsa-miR-512-3p|0|0|22M|12A9 3.0 -hsa-miR-512-3p|0|0|22M|17A4 5.0 -hsa-miR-512-3p|0|0|22M|21C 4.0 -hsa-miR-512-3p|0|0|22M|21C0 1.0 -hsa-miR-512-3p 3.0 -hsa-miR-512-3p|0|1|23M|21C0C0 2.0 -hsa-miR-512-3p|0|1|23M|22C 4.0 -hsa-miR-512-3p|0|1|23M|22C0 1.0 -hsa-miR-512-3p|0|1|23M|3T18C0 2.0 -hsa-miR-512-5p|1|-1|21M|21 3.0 -hsa-miR-512-5p|1|-2|20M|20 3.0 -hsa-miR-512-5p|1|0|22M|22 3.0 -hsa-miR-515-3p|0|-1|21M|21 3.0 -hsa-miR-516a-5p|0|-1|22M|22 3.0 -hsa-miR-516a-5p|1|-1|21M|21 7.0 -hsa-miR-516b-5p|0|-3|19M|18C 2.0 -hsa-miR-516b-5p|0|-3|19M|18C0 1.0 -hsa-miR-516b-5p|0|0|22M|10A11 3.0 -hsa-miR-516b-5p 3.0 -hsa-miR-517-5p|-1|0|23M|22T 15.0 -hsa-miR-517-5p|-1|0|23M|22T0 2.0 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 3.0 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 -hsa-miR-517a-3p|0|-1|21M|21 2.0 -hsa-miR-517a-3p 2.0 -hsa-miR-517b-3p|0|-1|21M|21 1.0 -hsa-miR-517b-3p 1.0 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 2.0 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 6.0 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 3.0 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 9.0 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 9.0 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 9.0 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 9.0 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 9.0 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 9.0 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 6.0 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 3.0 +hsa-miR-512-3p 9.0 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 2.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 3.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 1.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 3.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 1.0 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 3.0 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 2.0 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 9.0 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 9.0 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 9.0 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 9.0 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 9.0 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 9.0 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 6.0 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 3.0 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 9.0 +hsa-miR-516b-5p 9.0 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 3.0 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 2.0 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 9.0 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 9.0 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 6.0 +hsa-miR-517a-3p 6.0 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 3.0 +hsa-miR-517b-3p 3.0 hsa-miR-518b 1.0 -hsa-miR-518c-5p|1|-1|21M|21 1.0 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 -hsa-miR-518c-5p|1|0|22M|22 1.0 -hsa-miR-518d-5p|0|-1|21M|20T 1.0 -hsa-miR-518d-5p|0|-1|21M|20T0 1.0 -hsa-miR-518d-5p|0|-1|21M|21 10.0 -hsa-miR-518d-5p|0|-1|21M|3T16T0 1.0 -hsa-miR-518d-5p|0|-2|20M|20 10.0 -hsa-miR-518d-5p|0|-3|19M|19 2.0 -hsa-miR-518d-5p 8.0 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 1.0 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 1.0 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 2.0 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 1.0 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 2.0 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 2.0 +hsa-miR-518d-5p 2.0 hsa-miR-518e-3p 1.0 -hsa-miR-518e-5p|0|-1|21M|19C0T0 1.0 -hsa-miR-518e-5p|0|-1|21M|21 11.0 -hsa-miR-518e-5p|0|-2|20M|19C 1.0 -hsa-miR-518e-5p|0|-3|19M|19 1.0 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 1.0 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 1.0 hsa-miR-518e-5p 1.0 -hsa-miR-518e-5p|0|1|23M|23 1.0 -hsa-miR-518f-5p|0|-1|21M|20T 1.0 -hsa-miR-518f-5p|0|-1|21M|21 1.0 -hsa-miR-518f-5p|0|-1|21M|3T16T0 1.0 -hsa-miR-518f-5p|0|-2|20M|20 1.0 -hsa-miR-518f-5p|0|-3|19M|19 1.0 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 1.0 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 1.0 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.0 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 1.0 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 1.0 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 1.0 hsa-miR-518f-5p 1.0 -hsa-miR-519a-3p|0|0|22M|3G18 5.0 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 -hsa-miR-519a-5p|-1|-1|22M|22 1.0 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 -hsa-miR-519a-5p|0|-1|21M|19C0T0 1.0 -hsa-miR-519a-5p|0|-1|21M|21 12.0 -hsa-miR-519a-5p|0|-2|20M|19C 1.0 -hsa-miR-519a-5p|0|-2|20M|19C0 1.0 -hsa-miR-519a-5p|0|-3|19M|19 2.0 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 9.0 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 1.0 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.0 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 2.0 hsa-miR-519a-5p 2.0 -hsa-miR-519a-5p|0|1|23M|23 2.0 -hsa-miR-519b-5p|0|-1|21M|19C0T0 1.0 -hsa-miR-519b-5p|0|-1|21M|21 2.0 -hsa-miR-519b-5p|0|-2|20M|19C 11.0 -hsa-miR-519b-5p|0|-2|20M|19C0 1.0 -hsa-miR-519b-5p|0|-3|19M|19 2.0 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 2.0 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 1.0 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.0 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 2.0 hsa-miR-519b-5p 2.0 -hsa-miR-519b-5p|0|1|23M|23 2.0 -hsa-miR-519c-5p|0|-1|21M|19C0T0 1.0 -hsa-miR-519c-5p|0|-1|21M|21 2.0 -hsa-miR-519c-5p|0|-2|20M|19C 1.0 -hsa-miR-519c-5p|0|-2|20M|19C0 1.0 -hsa-miR-519c-5p|0|-3|19M|19 2.0 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 2.0 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 1.0 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.0 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 2.0 hsa-miR-519c-5p 2.0 -hsa-miR-519c-5p|0|1|23M|23 12.0 -hsa-miR-519d-3p|0|-1|21M|21 1.0 -hsa-miR-519d-3p|0|-2|20M|20 1.0 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 2.0 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 1.0 hsa-miR-520a-3p 1.0 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 -hsa-miR-520a-3p|0|1|23M|22T 1.0 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 -hsa-miR-520a-5p|0|0|21M|20T 1.0 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 hsa-miR-520a-5p 1.0 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 1.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 1.0 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 1.0 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 -hsa-miR-520b-3p|-1|-1|21M|21 2.0 -hsa-miR-520b-3p|0|1|22M|22 1.0 -hsa-miR-520c-3p|-1|-2|21M|21 2.0 -hsa-miR-520c-3p 2.0 -hsa-miR-520c-5p|0|-1|21M|20T 1.0 -hsa-miR-520c-5p|0|-1|21M|20T0 1.0 -hsa-miR-520c-5p|0|-1|21M|21 2.0 -hsa-miR-520c-5p|0|-1|21M|3T16T0 1.0 -hsa-miR-520c-5p|0|-2|20M|20 2.0 -hsa-miR-520c-5p|0|-3|19M|19 10.0 -hsa-miR-520c-5p 8.0 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 1.0 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 1.0 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 2.0 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 3.0 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 2.0 +hsa-miR-520c-3p 6.0 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 1.0 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 1.0 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 2.0 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 1.0 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 2.0 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 2.0 +hsa-miR-520c-5p 2.0 hsa-miR-520e-3p 1.0 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 -hsa-miR-520g-3p|1|-2|21M|21 1.0 -hsa-miR-520g-3p|1|0|23M|23 1.0 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 -hsa-miR-520h|1|0|21M|21 2.0 -hsa-miR-522-3p|0|0|22M|1A20 1.0 -hsa-miR-522-5p|0|-1|21M|19C0T0 1.0 -hsa-miR-522-5p|0|-1|21M|21 2.0 -hsa-miR-522-5p|0|-2|20M|19C 1.0 -hsa-miR-522-5p|0|-2|20M|19C0 1.0 -hsa-miR-522-5p|0|-3|19M|19 2.0 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 3.0 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 6.0 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 1.0 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.0 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 2.0 hsa-miR-522-5p 2.0 -hsa-miR-522-5p|0|1|23M|23 2.0 -hsa-miR-523-5p|0|-1|21M|19C0T0 1.0 -hsa-miR-523-5p|0|-1|21M|21 2.0 -hsa-miR-523-5p|0|-2|20M|19C 1.0 -hsa-miR-523-5p|0|-2|20M|19C0 1.0 -hsa-miR-523-5p|0|-3|19M|19 12.0 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 2.0 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 1.0 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.0 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 1.0 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 2.0 hsa-miR-523-5p 2.0 -hsa-miR-523-5p|0|1|23M|23 2.0 -hsa-miR-524-5p|0|-1|21M|21 1.0 -hsa-miR-524-5p|0|-2|20M|20 1.0 -hsa-miR-525-5p|0|-1|20M|20 1.0 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 2.0 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 1.0 hsa-miR-525-5p 1.0 -hsa-miR-526a-5p|0|-1|21M|20T 2.0 -hsa-miR-526a-5p|0|-1|21M|20T0 18.0 -hsa-miR-526a-5p|0|-1|21M|21 4.0 -hsa-miR-526a-5p|0|-1|21M|3T16T0 2.0 -hsa-miR-526a-5p|0|-2|20M|20 4.0 -hsa-miR-526a-5p|0|-3|19M|19 12.0 -hsa-miR-526a-5p 15.0 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 2.0 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 2.0 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 4.0 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 2.0 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 4.0 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 4.0 +hsa-miR-526a-5p 3.0 diff --git a/scripts/tests/files/read_ids_iso_mirna_quantification b/scripts/tests/files/read_ids_iso_mirna_quantification index 2246a1d..18bab50 100644 --- a/scripts/tests/files/read_ids_iso_mirna_quantification +++ b/scripts/tests/files/read_ids_iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 709268-1_1 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 709268-1_1 hsa-miR-1323 1.0 528546-1_1 hsa-miR-371a-5p 1.0 270342-1_1 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 840419-1_1 -hsa-miR-371b-3p|0|-1|22M|22 2.0 120522-2_1 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 299969-1_1 -hsa-miR-372-3p|0|-1|22M|22 4.0 67825-4_1 -hsa-miR-372-3p|0|-1|22M|3G18 3.0 90583-3_1 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 629861-1_1 -hsa-miR-372-3p|0|0|23M|22T 2.0 120521-2_1 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 840419-1_1 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 120522-2_1 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 299969-1_1 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 67825-4_1 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 90583-3_1 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 629861-1_1 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 120521-2_1 hsa-miR-372-3p 1.0 739110-1_1 -hsa-miR-372-3p|0|0|23M|3G19 1.0 270338-1_1 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 267649-1_1 -hsa-miR-372-3p|1|0|22M|22 1.0 313132-1_1 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 270337-1_1 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 270338-1_1 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 267649-1_1 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 313132-1_1 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 270337-1_1 hsa-miR-373-3p 2.0 188149-2_1 hsa-miR-498-5p 1.0 270393-1_1 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 610105-1_2;610105-1_2 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 645839-1_3;645839-1_3 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 645839-1_3 -hsa-miR-512-3p|0|-1|21M|21 4.0 67830-4_3;67830-4_3;67830-4_3 -hsa-miR-512-3p|0|-1|21M|7G13 1.0 535182-1_3;535182-1_3;535182-1_3 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 766380-1_3;766380-1_3;766380-1_3 -hsa-miR-512-3p|0|-2|20M|20 4.0 67831-4_3;67831-4_3;67831-4_3 -hsa-miR-512-3p|0|0|22M|12A9 1.0 270395-1_3;270395-1_3;270395-1_3 -hsa-miR-512-3p|0|0|22M|17A4 1.0 773136-1_3;773136-1_3;773136-1_3 -hsa-miR-512-3p|0|0|22M|21C 2.0 102065-3_3;102065-3_3 -hsa-miR-512-3p|0|0|22M|21C0 1.0 102065-3_3 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 610105-1_2;610105-1_2 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 645839-1_3;645839-1_3 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 645839-1_3 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 67830-4_3;67830-4_3;67830-4_3 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 535182-1_3;535182-1_3;535182-1_3 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 766380-1_3;766380-1_3;766380-1_3 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 67831-4_3;67831-4_3;67831-4_3 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 270395-1_3;270395-1_3;270395-1_3 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 773136-1_3;773136-1_3;773136-1_3 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 102065-3_3;102065-3_3 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 102065-3_3 hsa-miR-512-3p 9.0 37896-9_3;37896-9_3;37896-9_3 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 334943-1_2;334943-1_2 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 270396-1_3;270401-1_2;270396-1_3;270401-1_2 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 270396-1_3 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 673650-1_2;673650-1_2 -hsa-miR-512-5p|1|-1|21M|21 2.0 150819-2_3;150819-2_3;150819-2_3 -hsa-miR-512-5p|1|-2|20M|20 1.0 270402-1_3;270402-1_3;270402-1_3 -hsa-miR-512-5p|1|0|22M|22 1.0 752875-1_3;752875-1_3;752875-1_3 -hsa-miR-515-3p|0|-1|21M|21 1.0 369314-1_3;369314-1_3;369314-1_3 -hsa-miR-516a-5p|0|-1|22M|22 6.0 54840-6_3;54840-6_3;54840-6_3 -hsa-miR-516a-5p|1|-1|21M|21 1.0 423555-1_3;423555-1_3;423555-1_3 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 270365-1_3;270365-1_3 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 270365-1_3 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 270366-1_3;270366-1_3;270366-1_3 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 334943-1_2;334943-1_2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 270401-1_2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 270401-1_2 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 673650-1_2;673650-1_2 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 150819-2_3;150819-2_3;150819-2_3 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 270402-1_3;270402-1_3;270402-1_3 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 752875-1_3;752875-1_3;752875-1_3 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 369314-1_3;369314-1_3;369314-1_3 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 54840-6_3;54840-6_3;54840-6_3 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 423555-1_3;423555-1_3;423555-1_3 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 270365-1_3;270365-1_3 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 270365-1_3 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 270366-1_3;270366-1_3;270366-1_3 hsa-miR-516b-5p 3.0 86082-3_3;86082-3_3;86082-3_3 -hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 270359-1_5;270359-1_5;270359-1_5 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 270359-1_5;270359-1_5 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 752904-1_3;752904-1_3;752904-1_3 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 105051-3_3;105051-3_3;105051-3_3 -hsa-miR-517a-3p|0|-1|21M|21 1.3333333333333333 120530-2_3;120530-2_3 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 270359-1_5;270359-1_5;270359-1_5 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 270359-1_5;270359-1_5 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 752904-1_3;752904-1_3;752904-1_3 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 105051-3_3;105051-3_3;105051-3_3 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 120530-2_3;120530-2_3 hsa-miR-517a-3p 2.6666666666666665 67957-4_3;67957-4_3 -hsa-miR-517b-3p|0|-1|21M|21 0.6666666666666666 120530-2_3 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 120530-2_3 hsa-miR-517b-3p 1.3333333333333333 67957-4_3 hsa-miR-518b 1.0 447402-1_1 -hsa-miR-518c-5p|1|-1|21M|21 1.0 270377-1_1 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 751085-1_1 -hsa-miR-518c-5p|1|0|22M|22 1.0 270378-1_1 -hsa-miR-518d-5p|0|-1|21M|20T 0.2222222222222222 120527-2_9 -hsa-miR-518d-5p|0|-1|21M|20T0 0.2222222222222222 120527-2_9 -hsa-miR-518d-5p|0|-1|21M|21 0.6666666666666666 95680-3_9;95680-3_9 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 270379-1_5 -hsa-miR-518d-5p|0|-2|20M|20 0.4444444444444444 139675-2_9;139675-2_9 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 531738-1_9;531738-1_9 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 270377-1_1 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 751085-1_1 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 270378-1_1 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 95680-3_9;95680-3_9 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 139675-2_9;139675-2_9 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 531738-1_9;531738-1_9 hsa-miR-518d-5p 0.2857142857142857 270381-1_7;270381-1_7 hsa-miR-518e-3p 1.0 270360-1_1 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 676180-1_6 -hsa-miR-518e-5p|0|-1|21M|21 2.1818181818181817 18915-24_11 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 270361-1_11 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 630277-1_11 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 18915-24_11 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 630277-1_11 hsa-miR-518e-5p 0.36363636363636365 67687-4_11 -hsa-miR-518e-5p|0|1|23M|23 0.2727272727272727 84523-3_11 -hsa-miR-518f-5p|0|-1|21M|20T 0.2222222222222222 120527-2_9 -hsa-miR-518f-5p|0|-1|21M|21 0.3333333333333333 95680-3_9 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 270379-1_5 -hsa-miR-518f-5p|0|-2|20M|20 0.2222222222222222 139675-2_9 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 531738-1_9 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 84523-3_11 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 95680-3_9 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 139675-2_9 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 531738-1_9 hsa-miR-518f-5p 1.0 347693-1_1 -hsa-miR-519a-3p|0|0|22M|3G18 1.0 270348-1_3;270348-1_3;270348-1_3 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 270357-1_1 -hsa-miR-519a-5p|-1|-1|22M|22 5.0 58870-5_1 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 270354-1_1 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 676180-1_6 -hsa-miR-519a-5p|0|-1|21M|21 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 270361-1_11 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 270361-1_11 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 270348-1_3;270348-1_3;270348-1_3 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 270357-1_1 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 58870-5_1 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 270354-1_1 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 hsa-miR-519a-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-519a-5p|0|1|23M|23 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 676180-1_6 -hsa-miR-519b-5p|0|-1|21M|21 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-519b-5p|0|-2|20M|19C 0.09090909090909091 270361-1_11 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 270361-1_11 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 hsa-miR-519b-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-519b-5p|0|1|23M|23 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 676180-1_6 -hsa-miR-519c-5p|0|-1|21M|21 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 270361-1_11 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 270361-1_11 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 hsa-miR-519c-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-519c-5p|0|1|23M|23 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-519d-3p|0|-1|21M|21 1.0 270371-1_1 -hsa-miR-519d-3p|0|-2|20M|20 2.0 153079-2_1 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 270371-1_1 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 153079-2_1 hsa-miR-520a-3p 4.0 67829-4_1 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 655140-1_1 -hsa-miR-520a-3p|0|1|23M|22T 1.0 485300-1_1 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 729311-1_1 -hsa-miR-520a-5p|0|0|21M|20T 1.0 720817-1_1 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 655140-1_1 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 485300-1_1 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 729311-1_1 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 720817-1_1 hsa-miR-520a-5p 2.0 120535-2_1 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 228043-1_1 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 609803-1_1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 3.0 101076-3_1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 2.0 127441-2_1 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 3.0 103161-3_1 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 478794-1_1 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 744127-1_5;744127-1_5 -hsa-miR-520b-3p|0|1|22M|22 0.6666666666666666 120532-2_3 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 744127-1_5;744127-1_5 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 228043-1_1 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 609803-1_1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 101076-3_1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 127441-2_1 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 103161-3_1 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 478794-1_1 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 744127-1_5;744127-1_5 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 120532-2_3 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 744127-1_5;744127-1_5 hsa-miR-520c-3p 1.3333333333333333 120532-2_3;120532-2_3 -hsa-miR-520c-5p|0|-1|21M|20T 0.2222222222222222 120527-2_9 -hsa-miR-520c-5p|0|-1|21M|20T0 0.2222222222222222 120527-2_9 -hsa-miR-520c-5p|0|-1|21M|21 0.6666666666666666 95680-3_9;95680-3_9 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 270379-1_5 -hsa-miR-520c-5p|0|-2|20M|20 0.4444444444444444 139675-2_9;139675-2_9 -hsa-miR-520c-5p|0|-3|19M|19 0.2222222222222222 531738-1_9;531738-1_9 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 95680-3_9;95680-3_9 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 139675-2_9;139675-2_9 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 531738-1_9;531738-1_9 hsa-miR-520c-5p 0.2857142857142857 270381-1_7;270381-1_7 hsa-miR-520e-3p 1.0 361022-1_1 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 772976-1_1 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 270368-1_3 -hsa-miR-520g-3p|1|0|23M|23 1.0 270369-1_1 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 138559-2_2 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 270368-1_3;270368-1_3 -hsa-miR-522-3p|0|0|22M|1A20 1.0 270358-1_1 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 676180-1_6 -hsa-miR-522-5p|0|-1|21M|21 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 270361-1_11 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 270361-1_11 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 772976-1_1 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 270368-1_3 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 270369-1_1 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 138559-2_2 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 270368-1_3;270368-1_3 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 270358-1_1 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 hsa-miR-522-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-522-5p|0|1|23M|23 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 676180-1_6 -hsa-miR-523-5p|0|-1|21M|21 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 270361-1_11 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 270361-1_11 -hsa-miR-523-5p|0|-3|19M|19 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 hsa-miR-523-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-523-5p|0|1|23M|23 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-524-5p|0|-1|21M|21 1.0 270375-1_1 -hsa-miR-524-5p|0|-2|20M|20 1.0 270376-1_1 -hsa-miR-525-5p|0|-1|20M|20 5.0 57516-5_1 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 270375-1_1 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 270376-1_1 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 57516-5_1 hsa-miR-525-5p 3.0 102026-3_1 -hsa-miR-526a-5p|0|-1|21M|20T 0.4444444444444444 120527-2_9;120527-2_9 -hsa-miR-526a-5p|0|-1|21M|20T0 0.4444444444444444 120527-2_9;120527-2_9 -hsa-miR-526a-5p|0|-1|21M|21 1.3333333333333333 95680-3_9;95680-3_9;95680-3_9;95680-3_9 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 270379-1_5;270379-1_5 -hsa-miR-526a-5p|0|-2|20M|20 0.8888888888888888 139675-2_9;139675-2_9;139675-2_9;139675-2_9 -hsa-miR-526a-5p|0|-3|19M|19 0.4444444444444444 531738-1_9;531738-1_9;531738-1_9;531738-1_9 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 120527-2_9;120527-2_9 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 120527-2_9;120527-2_9 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 95680-3_9;95680-3_9;95680-3_9;95680-3_9 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 270379-1_5;270379-1_5 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 139675-2_9;139675-2_9;139675-2_9;139675-2_9 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 531738-1_9;531738-1_9;531738-1_9;531738-1_9 hsa-miR-526a-5p 0.42857142857142855 270381-1_7;270381-1_7;270381-1_7 diff --git a/scripts/tests/files/reads_ids_iso_mirna_quantification b/scripts/tests/files/reads_ids_iso_mirna_quantification new file mode 100644 index 0000000..18bab50 --- /dev/null +++ b/scripts/tests/files/reads_ids_iso_mirna_quantification @@ -0,0 +1,160 @@ +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 709268-1_1 +hsa-miR-1323 1.0 528546-1_1 +hsa-miR-371a-5p 1.0 270342-1_1 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 840419-1_1 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 120522-2_1 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 299969-1_1 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 67825-4_1 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 90583-3_1 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 629861-1_1 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 120521-2_1 +hsa-miR-372-3p 1.0 739110-1_1 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 270338-1_1 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 267649-1_1 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 313132-1_1 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 270337-1_1 +hsa-miR-373-3p 2.0 188149-2_1 +hsa-miR-498-5p 1.0 270393-1_1 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 610105-1_2;610105-1_2 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 645839-1_3;645839-1_3 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 645839-1_3 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 67830-4_3;67830-4_3;67830-4_3 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 535182-1_3;535182-1_3;535182-1_3 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 766380-1_3;766380-1_3;766380-1_3 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 67831-4_3;67831-4_3;67831-4_3 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 270395-1_3;270395-1_3;270395-1_3 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 773136-1_3;773136-1_3;773136-1_3 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 102065-3_3;102065-3_3 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 102065-3_3 +hsa-miR-512-3p 9.0 37896-9_3;37896-9_3;37896-9_3 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 334943-1_2;334943-1_2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 270401-1_2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 270401-1_2 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 673650-1_2;673650-1_2 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 150819-2_3;150819-2_3;150819-2_3 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 270402-1_3;270402-1_3;270402-1_3 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 752875-1_3;752875-1_3;752875-1_3 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 369314-1_3;369314-1_3;369314-1_3 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 54840-6_3;54840-6_3;54840-6_3 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 423555-1_3;423555-1_3;423555-1_3 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 270365-1_3;270365-1_3 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 270365-1_3 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 270366-1_3;270366-1_3;270366-1_3 +hsa-miR-516b-5p 3.0 86082-3_3;86082-3_3;86082-3_3 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 270359-1_5;270359-1_5;270359-1_5 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 270359-1_5;270359-1_5 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 752904-1_3;752904-1_3;752904-1_3 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 105051-3_3;105051-3_3;105051-3_3 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 120530-2_3;120530-2_3 +hsa-miR-517a-3p 2.6666666666666665 67957-4_3;67957-4_3 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 120530-2_3 +hsa-miR-517b-3p 1.3333333333333333 67957-4_3 +hsa-miR-518b 1.0 447402-1_1 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 270377-1_1 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 751085-1_1 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 270378-1_1 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 95680-3_9;95680-3_9 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 139675-2_9;139675-2_9 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 531738-1_9;531738-1_9 +hsa-miR-518d-5p 0.2857142857142857 270381-1_7;270381-1_7 +hsa-miR-518e-3p 1.0 270360-1_1 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 18915-24_11 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 630277-1_11 +hsa-miR-518e-5p 0.36363636363636365 67687-4_11 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 84523-3_11 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 95680-3_9 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 139675-2_9 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 531738-1_9 +hsa-miR-518f-5p 1.0 347693-1_1 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 270348-1_3;270348-1_3;270348-1_3 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 270357-1_1 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 58870-5_1 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 270354-1_1 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-519a-5p 0.7272727272727273 67687-4_11;67687-4_11 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-519b-5p 0.7272727272727273 67687-4_11;67687-4_11 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-519c-5p 0.7272727272727273 67687-4_11;67687-4_11 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 270371-1_1 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 153079-2_1 +hsa-miR-520a-3p 4.0 67829-4_1 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 655140-1_1 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 485300-1_1 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 729311-1_1 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 720817-1_1 +hsa-miR-520a-5p 2.0 120535-2_1 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 228043-1_1 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 609803-1_1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 101076-3_1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 127441-2_1 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 103161-3_1 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 478794-1_1 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 744127-1_5;744127-1_5 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 120532-2_3 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 744127-1_5;744127-1_5 +hsa-miR-520c-3p 1.3333333333333333 120532-2_3;120532-2_3 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 95680-3_9;95680-3_9 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 139675-2_9;139675-2_9 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 531738-1_9;531738-1_9 +hsa-miR-520c-5p 0.2857142857142857 270381-1_7;270381-1_7 +hsa-miR-520e-3p 1.0 361022-1_1 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 772976-1_1 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 270368-1_3 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 270369-1_1 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 138559-2_2 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 270368-1_3;270368-1_3 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 270358-1_1 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-522-5p 0.7272727272727273 67687-4_11;67687-4_11 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 +hsa-miR-523-5p 0.7272727272727273 67687-4_11;67687-4_11 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 270375-1_1 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 270376-1_1 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 57516-5_1 +hsa-miR-525-5p 3.0 102026-3_1 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 120527-2_9;120527-2_9 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 120527-2_9;120527-2_9 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 95680-3_9;95680-3_9;95680-3_9;95680-3_9 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 270379-1_5;270379-1_5 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 139675-2_9;139675-2_9;139675-2_9;139675-2_9 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 531738-1_9;531738-1_9;531738-1_9;531738-1_9 +hsa-miR-526a-5p 0.42857142857142855 270381-1_7;270381-1_7;270381-1_7 diff --git a/scripts/tests/files/uncollapsed_iso_mirna_quantification b/scripts/tests/files/uncollapsed_iso_mirna_quantification new file mode 100644 index 0000000..366d6a4 --- /dev/null +++ b/scripts/tests/files/uncollapsed_iso_mirna_quantification @@ -0,0 +1,160 @@ +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 +hsa-miR-1323 1.0 +hsa-miR-371a-5p 1.0 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 1.0 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 1.0 +hsa-miR-372-3p 1.0 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-373-3p 1.0 +hsa-miR-498-5p 1.0 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 1.0 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 1.0 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 0.6666666666666666 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 0.3333333333333333 +hsa-miR-512-3p 1.0 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 1.0 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 1.0 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 +hsa-miR-516b-5p 1.0 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 1.0 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 +hsa-miR-517a-3p 0.6666666666666666 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.3333333333333333 +hsa-miR-517b-3p 0.3333333333333333 +hsa-miR-518b 1.0 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.2222222222222222 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 +hsa-miR-518d-5p 0.2857142857142857 +hsa-miR-518e-3p 1.0 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.09090909090909091 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 +hsa-miR-518e-5p 0.09090909090909091 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.09090909090909091 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.1111111111111111 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.1111111111111111 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 +hsa-miR-518f-5p 1.0 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-519a-5p 0.18181818181818182 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-519b-5p 0.18181818181818182 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-519c-5p 0.18181818181818182 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 1.0 +hsa-miR-520a-3p 1.0 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 +hsa-miR-520a-5p 1.0 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 1.0 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 1.0 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.3333333333333333 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 +hsa-miR-520c-3p 0.6666666666666666 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 +hsa-miR-520c-5p 0.2857142857142857 +hsa-miR-520e-3p 1.0 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 0.5 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-522-5p 0.18181818181818182 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 +hsa-miR-523-5p 0.18181818181818182 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 1.0 +hsa-miR-525-5p 1.0 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 +hsa-miR-526a-5p 0.42857142857142855 diff --git a/scripts/tests/files/uncollapsed_missing_nh_iso_mirna_quantification b/scripts/tests/files/uncollapsed_missing_nh_iso_mirna_quantification index 1fbfec5..4fce0fb 100644 --- a/scripts/tests/files/uncollapsed_missing_nh_iso_mirna_quantification +++ b/scripts/tests/files/uncollapsed_missing_nh_iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 1 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 1 hsa-miR-1323 1.0 1 hsa-miR-371a-5p 1.0 1 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 1 -hsa-miR-371b-3p|0|-1|22M|22 1.0 1 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 1 -hsa-miR-372-3p|0|-1|22M|22 1.0 1 -hsa-miR-372-3p|0|-1|22M|3G18 1.0 1 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 1 -hsa-miR-372-3p|0|0|23M|22T 1.0 1 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 1 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 1.0 1 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 1 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 1.0 1 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 1.0 1 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 1 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 1.0 1 hsa-miR-372-3p 1.0 1 -hsa-miR-372-3p|0|0|23M|3G19 1.0 1 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 1 -hsa-miR-372-3p|1|0|22M|22 1.0 1 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 1 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 1 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 1 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 1 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 1 hsa-miR-373-3p 1.0 1 hsa-miR-498-5p 1.0 1 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 2 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 2 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 1 -hsa-miR-512-3p|0|-1|21M|21 1.0 3 -hsa-miR-512-3p|0|-1|21M|7G13 1.6666666666666665 3 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 3 -hsa-miR-512-3p|0|-2|20M|20 1.6666666666666665 3 -hsa-miR-512-3p|0|0|22M|12A9 1.0 3 -hsa-miR-512-3p|0|0|22M|17A4 1.6666666666666665 3 -hsa-miR-512-3p|0|0|22M|21C 1.3333333333333333 2 -hsa-miR-512-3p|0|0|22M|21C0 0.3333333333333333 1 -hsa-miR-512-3p 1.0 3 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 2 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 4 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 1 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 2 -hsa-miR-512-5p|1|-1|21M|21 1.0 3 -hsa-miR-512-5p|1|-2|20M|20 1.0 3 -hsa-miR-512-5p|1|0|22M|22 1.0 3 -hsa-miR-515-3p|0|-1|21M|21 1.0 3 -hsa-miR-516a-5p|0|-1|22M|22 1.0 3 -hsa-miR-516a-5p|1|-1|21M|21 2.333333333333333 3 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 2 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 1 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 3 -hsa-miR-516b-5p 1.0 3 -hsa-miR-517-5p|-1|0|23M|22T 3.0 3 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 2 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 3 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 1.0 3 -hsa-miR-517a-3p|0|-1|21M|21 0.6666666666666666 2 -hsa-miR-517a-3p 0.6666666666666666 2 -hsa-miR-517b-3p|0|-1|21M|21 0.3333333333333333 1 -hsa-miR-517b-3p 0.3333333333333333 1 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 2 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 2.0 2 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 1.0 1 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 3.0 3 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 3.0 3 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 3.0 3 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 3.0 3 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 3.0 3 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 3.0 3 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 2 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 1 +hsa-miR-512-3p 3.0 3 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 2 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 1.0 1 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 1 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 1.0 1 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 1 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 1.0 1 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 2 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 3.0 3 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 3.0 3 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 3.0 3 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 3.0 3 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 3.0 3 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 3.0 3 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 2.0 2 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 1.0 1 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 3.0 3 +hsa-miR-516b-5p 3.0 3 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 3 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 2 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 3.0 3 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 3 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 2.0 2 +hsa-miR-517a-3p 2.0 2 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.0 1 +hsa-miR-517b-3p 1.0 1 hsa-miR-518b 1.0 1 -hsa-miR-518c-5p|1|-1|21M|21 1.0 1 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 1 -hsa-miR-518c-5p|1|0|22M|22 1.0 1 -hsa-miR-518d-5p|0|-1|21M|20T 0.1111111111111111 1 -hsa-miR-518d-5p|0|-1|21M|20T0 0.1111111111111111 1 -hsa-miR-518d-5p|0|-1|21M|21 1.1111111111111112 2 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 1 -hsa-miR-518d-5p|0|-2|20M|20 1.1111111111111112 2 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 2 -hsa-miR-518d-5p 1.1428571428571428 2 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 1 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 1 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 1 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 1 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 1 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.2222222222222222 2 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 1 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.2222222222222222 2 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 2 +hsa-miR-518d-5p 0.2857142857142857 2 hsa-miR-518e-3p 1.0 1 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 1 -hsa-miR-518e-5p|0|-1|21M|21 1.0 1 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 1 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 1 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 1 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.09090909090909091 1 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 1 hsa-miR-518e-5p 0.09090909090909091 1 -hsa-miR-518e-5p|0|1|23M|23 0.09090909090909091 1 -hsa-miR-518f-5p|0|-1|21M|20T 0.1111111111111111 1 -hsa-miR-518f-5p|0|-1|21M|21 0.1111111111111111 1 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 1 -hsa-miR-518f-5p|0|-2|20M|20 0.1111111111111111 1 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 1 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.09090909090909091 1 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 1 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.1111111111111111 1 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 1 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.1111111111111111 1 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 1 hsa-miR-518f-5p 1.0 1 -hsa-miR-519a-3p|0|0|22M|3G18 1.6666666666666665 3 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 1 -hsa-miR-519a-5p|-1|-1|22M|22 1.0 1 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 1 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 1 -hsa-miR-519a-5p|0|-1|21M|21 1.0909090909090908 2 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 1 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 1 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 2 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 3.0 3 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 1 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 1.0 1 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 1 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 1 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 2 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 2 hsa-miR-519a-5p 0.18181818181818182 2 -hsa-miR-519a-5p|0|1|23M|23 0.18181818181818182 2 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 1 -hsa-miR-519b-5p|0|-1|21M|21 0.18181818181818182 2 -hsa-miR-519b-5p|0|-2|20M|19C 1.0 1 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 1 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 2 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 2 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 1 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 2 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 2 hsa-miR-519b-5p 0.18181818181818182 2 -hsa-miR-519b-5p|0|1|23M|23 0.18181818181818182 2 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 1 -hsa-miR-519c-5p|0|-1|21M|21 0.18181818181818182 2 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 1 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 1 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 2 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 2 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 1 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 2 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 2 hsa-miR-519c-5p 0.18181818181818182 2 -hsa-miR-519c-5p|0|1|23M|23 1.0909090909090908 2 -hsa-miR-519d-3p|0|-1|21M|21 1.0 1 -hsa-miR-519d-3p|0|-2|20M|20 1.0 1 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 2 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 1 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 1.0 1 hsa-miR-520a-3p 1.0 1 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 1 -hsa-miR-520a-3p|0|1|23M|22T 1.0 1 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 1 -hsa-miR-520a-5p|0|0|21M|20T 1.0 1 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 1 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 1 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 1 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 1 hsa-miR-520a-5p 1.0 1 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 1 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 1.0 1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 1.0 1 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 1.0 1 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 1 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 2 -hsa-miR-520b-3p|0|1|22M|22 0.3333333333333333 1 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 2 -hsa-miR-520c-3p 0.6666666666666666 2 -hsa-miR-520c-5p|0|-1|21M|20T 0.1111111111111111 1 -hsa-miR-520c-5p|0|-1|21M|20T0 0.1111111111111111 1 -hsa-miR-520c-5p|0|-1|21M|21 0.2222222222222222 2 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 1 -hsa-miR-520c-5p|0|-2|20M|20 0.2222222222222222 2 -hsa-miR-520c-5p|0|-3|19M|19 1.1111111111111112 2 -hsa-miR-520c-5p 1.1428571428571428 2 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 1 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 1.0 1 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 1.0 1 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 1.0 1 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 1 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 2 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 1.0 1 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 2 +hsa-miR-520c-3p 2.0 2 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 1 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.1111111111111111 1 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.2222222222222222 2 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 1 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 2 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 2 +hsa-miR-520c-5p 0.2857142857142857 2 hsa-miR-520e-3p 1.0 1 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 1 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 1 -hsa-miR-520g-3p|1|0|23M|23 1.0 1 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 0.5 1 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 2 -hsa-miR-522-3p|0|0|22M|1A20 1.0 1 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 1 -hsa-miR-522-5p|0|-1|21M|21 0.18181818181818182 2 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 1 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 1 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 2 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 1 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 1.0 1 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 1 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 0.5 1 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 2.0 2 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 1 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 1 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 2 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 2 hsa-miR-522-5p 0.18181818181818182 2 -hsa-miR-522-5p|0|1|23M|23 0.18181818181818182 2 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 1 -hsa-miR-523-5p|0|-1|21M|21 0.18181818181818182 2 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 1 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 1 -hsa-miR-523-5p|0|-3|19M|19 1.0909090909090908 2 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 2 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 1 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 0.18181818181818182 2 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 1 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 2 hsa-miR-523-5p 0.18181818181818182 2 -hsa-miR-523-5p|0|1|23M|23 0.18181818181818182 2 -hsa-miR-524-5p|0|-1|21M|21 1.0 1 -hsa-miR-524-5p|0|-2|20M|20 1.0 1 -hsa-miR-525-5p|0|-1|20M|20 1.0 1 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.18181818181818182 2 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 1 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 1 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 1.0 1 hsa-miR-525-5p 1.0 1 -hsa-miR-526a-5p|0|-1|21M|20T 0.2222222222222222 2 -hsa-miR-526a-5p|0|-1|21M|20T0 2.0 2 -hsa-miR-526a-5p|0|-1|21M|21 0.4444444444444444 4 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 2 -hsa-miR-526a-5p|0|-2|20M|20 0.4444444444444444 4 -hsa-miR-526a-5p|0|-3|19M|19 1.3333333333333335 4 -hsa-miR-526a-5p 2.142857142857143 3 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 2 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 2 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.4444444444444444 4 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 2 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 4 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 4 +hsa-miR-526a-5p 0.42857142857142855 3 diff --git a/scripts/tests/files/xn_tag_iso_mirna_quantification b/scripts/tests/files/xn_tag_iso_mirna_quantification index 634dfa9..984b6d8 100644 --- a/scripts/tests/files/xn_tag_iso_mirna_quantification +++ b/scripts/tests/files/xn_tag_iso_mirna_quantification @@ -1,157 +1,160 @@ -hsa-miR-1323|0|-1|21M|21 1.0 +hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 hsa-miR-1323 1.0 hsa-miR-371a-5p 1.0 -hsa-miR-371a-5p|0|3|23M|17A3T0C0 1.0 -hsa-miR-371b-3p|0|-1|22M|22 2.0 -hsa-miR-372-3p|0|-1|22M|0A0A2T17 1.0 -hsa-miR-372-3p|0|-1|22M|22 4.0 -hsa-miR-372-3p|0|-1|22M|3G18 3.0 -hsa-miR-372-3p|0|0|23M|1A20T0 1.0 -hsa-miR-372-3p|0|0|23M|22T 2.0 +hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 +hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 +hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 +hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 +hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 +hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 +hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 hsa-miR-372-3p 1.0 -hsa-miR-372-3p|0|0|23M|3G19 1.0 -hsa-miR-372-3p|1|0|21M1I1M|23 1.0 -hsa-miR-372-3p|1|0|22M|22 1.0 -hsa-miR-372-3p|1|0|4M1I18M|2G19 1.0 +hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 +hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 +hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 hsa-miR-373-3p 2.0 hsa-miR-498-5p 1.0 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4 1.0 -hsa-miR-512-3p|0|-1|21M|20T 0.6666666666666666 -hsa-miR-512-3p|0|-1|21M|20T0 0.3333333333333333 -hsa-miR-512-3p|0|-1|21M|21 4.0 -hsa-miR-512-3p|0|-1|21M|7G13 1.0 -hsa-miR-512-3p|0|-2|20M|12A7 1.0 -hsa-miR-512-3p|0|-2|20M|20 4.0 -hsa-miR-512-3p|0|0|22M|12A9 1.0 -hsa-miR-512-3p|0|0|22M|17A4 1.0 -hsa-miR-512-3p|0|0|22M|21C 2.0 -hsa-miR-512-3p|0|0|22M|21C0 1.0 +hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 +hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 +hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 +hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 +hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 +hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 +hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 +hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 +hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 +hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 +hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 hsa-miR-512-3p 9.0 -hsa-miR-512-3p|0|1|23M|21C0C0 1.0 -hsa-miR-512-3p|0|1|23M|22C 1.6666666666666665 -hsa-miR-512-3p|0|1|23M|22C0 0.3333333333333333 -hsa-miR-512-3p|0|1|23M|3T18C0 1.0 -hsa-miR-512-5p|1|-1|21M|21 2.0 -hsa-miR-512-5p|1|-2|20M|20 1.0 -hsa-miR-512-5p|1|0|22M|22 1.0 -hsa-miR-515-3p|0|-1|21M|21 1.0 -hsa-miR-516a-5p|0|-1|22M|22 6.0 -hsa-miR-516a-5p|1|-1|21M|21 1.0 -hsa-miR-516b-5p|0|-3|19M|18C 0.6666666666666666 -hsa-miR-516b-5p|0|-3|19M|18C0 0.3333333333333333 -hsa-miR-516b-5p|0|0|22M|10A11 1.0 +hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 +hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 +hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 +hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 +hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 +hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 +hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 +hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 +hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 +hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 +hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 +hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 hsa-miR-516b-5p 3.0 -hsa-miR-517-5p|-1|0|23M|22T 0.6000000000000001 -hsa-miR-517-5p|-1|0|23M|22T0 0.4 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13 1.0 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3 3.0 -hsa-miR-517a-3p|0|-1|21M|21 1.3333333333333333 +hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 +hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 +hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 +hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 +hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 hsa-miR-517a-3p 2.6666666666666665 -hsa-miR-517b-3p|0|-1|21M|21 0.6666666666666666 +hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 hsa-miR-517b-3p 1.3333333333333333 hsa-miR-518b 1.0 -hsa-miR-518c-5p|1|-1|21M|21 1.0 -hsa-miR-518c-5p|1|-2|20M|19C 1.0 -hsa-miR-518c-5p|1|0|22M|22 1.0 -hsa-miR-518d-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-518d-5p|0|-1|21M|20T0 0.2222222222222222 -hsa-miR-518d-5p|0|-1|21M|21 0.6666666666666666 -hsa-miR-518d-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-518d-5p|0|-2|20M|20 0.4444444444444444 -hsa-miR-518d-5p|0|-3|19M|19 0.2222222222222222 +hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 +hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 +hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 +hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 +hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 hsa-miR-518d-5p 0.2857142857142857 hsa-miR-518e-3p 1.0 -hsa-miR-518e-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-518e-5p|0|-1|21M|21 2.1818181818181817 -hsa-miR-518e-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-518e-5p|0|-3|19M|19 0.09090909090909091 +hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 +hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 hsa-miR-518e-5p 0.36363636363636365 -hsa-miR-518e-5p|0|1|23M|23 0.2727272727272727 -hsa-miR-518f-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-518f-5p|0|-1|21M|21 0.3333333333333333 -hsa-miR-518f-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-518f-5p|0|-2|20M|20 0.2222222222222222 -hsa-miR-518f-5p|0|-3|19M|19 0.1111111111111111 +hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 +hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 +hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 +hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 hsa-miR-518f-5p 1.0 -hsa-miR-519a-3p|0|0|22M|3G18 1.0 -hsa-miR-519a-5p|-1|-1|22M|21T 1.0 -hsa-miR-519a-5p|-1|-1|22M|22 5.0 -hsa-miR-519a-5p|-1|-3|20M|20 1.0 -hsa-miR-519a-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519a-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519a-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519a-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519a-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 +hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 +hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 +hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 +hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-519a-5p 0.7272727272727273 -hsa-miR-519a-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519b-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519b-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519b-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519b-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519b-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-519b-5p 0.7272727272727273 -hsa-miR-519b-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519c-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-519c-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-519c-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-519c-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-519c-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-519c-5p 0.7272727272727273 -hsa-miR-519c-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-519d-3p|0|-1|21M|21 1.0 -hsa-miR-519d-3p|0|-2|20M|20 2.0 +hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 +hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 hsa-miR-520a-3p 4.0 -hsa-miR-520a-3p|0|0|22M|3G18 1.0 -hsa-miR-520a-3p|0|1|23M|22T 1.0 -hsa-miR-520a-5p|0|0|21M|19C0T0 1.0 -hsa-miR-520a-5p|0|0|21M|20T 1.0 +hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 +hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 +hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 +hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 hsa-miR-520a-5p 2.0 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1 1.0 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1 1.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0 3.0 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0 2.0 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0 3.0 -hsa-miR-520a-5p|0|2|23M|19C0T1T0 1.0 -hsa-miR-520b-3p|-1|-1|21M|21 0.4 -hsa-miR-520b-3p|0|1|22M|22 0.6666666666666666 -hsa-miR-520c-3p|-1|-2|21M|21 0.4 +hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 +hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 +hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 +hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 +hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 +hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 +hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 +hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 hsa-miR-520c-3p 1.3333333333333333 -hsa-miR-520c-5p|0|-1|21M|20T 0.2222222222222222 -hsa-miR-520c-5p|0|-1|21M|20T0 0.2222222222222222 -hsa-miR-520c-5p|0|-1|21M|21 0.6666666666666666 -hsa-miR-520c-5p|0|-1|21M|3T16T0 0.2 -hsa-miR-520c-5p|0|-2|20M|20 0.4444444444444444 -hsa-miR-520c-5p|0|-3|19M|19 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 +hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 +hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 +hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 +hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 hsa-miR-520c-5p 0.2857142857142857 hsa-miR-520e-3p 1.0 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13 1.0 -hsa-miR-520g-3p|1|-2|21M|21 0.3333333333333333 -hsa-miR-520g-3p|1|0|23M|23 1.0 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8 1.0 -hsa-miR-520h|1|0|21M|21 0.6666666666666666 -hsa-miR-522-3p|0|0|22M|1A20 1.0 -hsa-miR-522-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-522-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-522-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-522-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-522-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 +hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 +hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 +hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 +hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 +hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 +hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-522-5p 0.7272727272727273 -hsa-miR-522-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-523-5p|0|-1|21M|19C0T0 0.16666666666666666 -hsa-miR-523-5p|0|-1|21M|21 4.363636363636363 -hsa-miR-523-5p|0|-2|20M|19C 0.09090909090909091 -hsa-miR-523-5p|0|-2|20M|19C0 0.09090909090909091 -hsa-miR-523-5p|0|-3|19M|19 0.18181818181818182 +hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 +hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 +hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 +hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 hsa-miR-523-5p 0.7272727272727273 -hsa-miR-523-5p|0|1|23M|23 0.5454545454545454 -hsa-miR-524-5p|0|-1|21M|21 1.0 -hsa-miR-524-5p|0|-2|20M|20 1.0 -hsa-miR-525-5p|0|-1|20M|20 5.0 +hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 +hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 +hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 +hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 hsa-miR-525-5p 3.0 -hsa-miR-526a-5p|0|-1|21M|20T 0.4444444444444444 -hsa-miR-526a-5p|0|-1|21M|20T0 0.4444444444444444 -hsa-miR-526a-5p|0|-1|21M|21 1.3333333333333333 -hsa-miR-526a-5p|0|-1|21M|3T16T0 0.4 -hsa-miR-526a-5p|0|-2|20M|20 0.8888888888888888 -hsa-miR-526a-5p|0|-3|19M|19 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 +hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 +hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 +hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 +hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 hsa-miR-526a-5p 0.42857142857142855 From 590b93dcc31acb810bd3f692d449de9b90883e27 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:19:20 +0200 Subject: [PATCH 28/42] revert: undo documetation branch merge --- README.md | 150 ++++++++++-------------------------------------------- 1 file changed, 28 insertions(+), 122 deletions(-) diff --git a/README.md b/README.md index 4c6c24d..2a8588d 100644 --- a/README.md +++ b/README.md @@ -15,10 +15,6 @@ _MIRFLOWZ_ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs. - [Expected output files](#expected-output-files) - [Creating a Snakemake report](#creating-a-snakemake-report) 3. [Workflow description](#workflow-description) - - [Prepare module](#prepare-module) - - [Map module](#map-module) - - [Quantify module](#quantify-module) - - [ASCII-style pileups module](#ascii-style-pileups-module) 4. [Contributing](#contributing) 5. [License](#license) 6. [Contact](#contact) @@ -44,8 +40,8 @@ For improved reproducibility and reusability of the workflow, as well as an easy means to run it on a high performance computing (HPC) cluster managed, e.g., by [Slurm][slurm], all steps of the workflow run inside isolated environments ([Singularity][singularity] containers or [Conda][conda] -environments). As a consequence, running this workflow has only a few -individual dependencies. These are managed by the package manager Conda, which +environments). As a consequence, running this workflow has only a few individual +dependencies. These are managed by the package manager Conda, which needs to be installed on your system before proceeding. If you do not already have Conda installed globally on your system, @@ -163,7 +159,7 @@ tested, you can go ahead and run the workflow on your samples. It is suggested to have all the input files for a given run (or hard links pointing to them) inside a dedicated directory, for instance under the _MIRFLOWZ_ root directory. This way, it is easier to keep the data together, -set up Singularity access to them and reproduce analyses. +reproduce an analysis and set up Singularity access to them. #### 1. Prepare a sample table @@ -214,8 +210,8 @@ There are 4 files you must provide: expected format. 5. **OPTIONAL**: A **BED6** file with regions for which to produce - [ASCII-style pileups][ascii-pileups]. If not provided, no pileups are - generated. See [here][bed-format] for the expected format. + [ASCII-style alignment pileups][ascii-pileups]. If not provided, no pileups + will be generated. See [here][bed-format] for the expected format. > General note: If you want to process the genome resources before use (e.g., > filtering), you can do that, but make sure the formats of any modified @@ -269,7 +265,9 @@ intermediate files generated during the process. The final outputs comprise: 1. A SAM file containing alignments intersecting a pri-miR locus. These alignments intersect with extended start and/or end positions specified in the provided pri-miR annotations. Please note that they may not contribute to the -final counting and may not appear in the final table. +final counting and may not appear in the final table. Alignments are discarded +if their start and/or end positions differ from the ends of the provided +pri-miR annotations by more bases than the extension used. 2. A SAM file containing alignments intersecting a mature miRNA locus. Similar to the previous file, these alignments intersect with extended start and/or end @@ -327,126 +325,33 @@ snakemake \ ## Workflow description -_MIRFLOWZ_ consists of a main `Snakefile` and four functional modules. In the -`Snakefile`, the configuration file is validated, and the various modules are -imported. In addition, a handler for both, a successful and a failed run are -set. If the workflow finishes without any errors, all the intermediate files -are removed, otherwise, a log file is created. To keep the intermediate files -upon completion, use the `--no-hooks` CLI argument when running the pipeline. - -The modules [(1)](#prepare-module) process the genome resources, -[(2)](#map-module) map and [(3)](#quantify-module) quantify the reads, and -[(4)](#ascii-style-pileups-module) generate pileups, as described in detail -below. - -> **NOTE:** _MIRFLOWZ_ uses the notation provided by miRBase (_i.e._ -> "miRNA primary transcript" for precursors and "miRNA" for the canonical -> mature miRNA). This implies that precursors are named "pri-miRs" across the -> workflow instead of pre-miR. This decision is made upon the lack of -> guarantee that "miRNA primary transcripts" are full pre-miR (and pre-miR -> only) sequences. - -### Prepare module - -The _MIRFLOWZ_ workflow initially processes and indexes the genome resources -provided by the user. The regions corresponding to mature miRNAs are extended -by a fixed but user-adjustable number of nucleotides on both sides to -accommodate isomiR species with shifted start and/or end positions. If -necessary, pri-miR loci are extended to adjust to the new miRNA coordinates. -In addition, to account for the different genomic locations a miRNA sequence -can be annotated, the name of these sequences are modified to have the format -`SPECIES-mir-NAME-#` for pri-miRs and `SPECIES-miR-NAME-#-ARM` or -`SPECIES-miR-NAME-#` for mature miRNAs with both or just one arm respectively, -where `#` is the replica number. - -### Map module - -The user-provided short-read small RNA-seq libraries undergo quality filtering -(skipped if libraries are provided in FASTA rather than FASTQ), followed by -adapter removal. The resulting reads are independently mapped to both the -genome and the transcriptome using two distinct aligners: Segemehl and our -in-house tool Oligomap. - -Segemehl implements a fast heuristic strategy that returns the alignment(s) -with the smallest edit distance. Oligomap, on the other hand, implements a -slower and more restricted approach that reports all the alignments with an -edit distance of at most 1. The combination of the fast and flexible results -and the strict selection ensures results with a higher fidelity than if only -one of the tools was to be used. - -Two merging steps are done in order to have all the alignments in a single -file. In the first one, the transcriptome and the genome mappings from both -aligners are fused and only those alignments with a smaller NH than the one -provided are kept. For the second step, transcriptomic coordinates are turned -into genomic ones and alignments are combined into a single file. Duplicate -alignments resulting from the partially redundant mapping strategy are -discarded and only the best alignments for each read are retained (_i.e._ the -ones with the smallest edit distance). In addition, and due to the alignment's -aggregation, a second filtering according to the new NH is performed. -If a read has been aligned beyond a specified threshold, it is removed due to -(1) performance reasons as the file size can rapidly increase, and (2) the fact -that each read contributes to each count `1/N` where `N` is the number of -genomic loci it aligns to and a large `N` makes the contribution negligible. - -A final filter is made to further increase the classification accuracy and -reduce the amount of multimappers. Given that isomiRs are known to present more -mismatches than InDels when compared to the canonical sequence they come from, -when addressing the multiple genomic locations a read has been mapped to, the -alignments with fewer InDels are kept. Note that some multimappers might still -be present if the number of InDels and mismatches is the same across -alignments. - -### Quantify module - -The filtered alignments are subsequently intersected with the user-provided, -pre-processed miRNA annotation files using BEDTools. Each alignment is -classified according to the miRNA species it fully intersects with in order -to do the counts. - -Counts are tabulated separately for reads consistent with either miRNA -precursors, mature miRNA and/or isomiRs, and all library counts are fused -into a single table. Note that an alignment is only counted towards a given -miRNA (or isomiR) species if one of its alignments fully falls within the -(previously extended) locus annotated for that miRNA. Specifically, reads -contribute with `1/N` for each miRNA for which that is the case, where `N` is -the total number of genomic loci the read aligns to. Under this criterion, the -precursor counts contain reads that intersect with its mature arm(s), its -hairpin sequence and/or the whole precursor itself. - -#### isomiRs notation - -A sequence is considered to be an isomiR if it has a shift on either end, an -InDel or a mismatch on its sequence when compared to the canonical miRNA it -maps and intersects with. - -_MIRFLOWZ_ employs an unambiguous notation to classify isomiRs using the -format `miRNA_name|5p-shift|3p-shift|CIGAR|MD|read_seq`, where `5p-shift` and -`3p-shift` represent the differences between the annotated mature miRNA -start and end positions and those of the read alignment, respectively. - -### ASCII-style pileups module - -Finally, to visualize the distribution of read alignments around miRNA -loci, ASCII-style alignment pileups are optionally generated for user-defined -regions of interest. - +The _MIRFLOWZ_ workflow first processes and indexes the user-provided genome +resources. Afterwards, the user-provided short read small-RNA-seq libraries will +be aligned separately against the genome and transcriptome. For increased +fidelity, two separated aligners, [Segemehl][segemehl] and our in-house tool +[Oligomap][oligomap], are used. All the resulting alignments are merged such +that only the best alignments of each read are kept (smallest edit distance). +Alignments are intersected with the user-provided, pre-processed miRNA +annotation file using [BEDTools][bedtools]. Counts are tabulated separately for +reads consistent with either miRNA precursors, mature miRNA and/or isomiRs. +Finally, ASCII-style alignment pileups are optionally generated for +user-defined regions of interest. + +> **NOTE:** For a detailed description of each rule, please, refer to the +> [workflow documentation](pipeline_documentation.md) The schema below is a visual representation of the individual workflow steps and how they are related: > ![rule-graph][rule-graph] -> **NOTE:** For an elaborated description of each rule along with some -> examples, please, refer to the -> [workflow documentation](pipeline_documentation.md). - ## Contributing _MIRFLOWZ_ is an open-source project which relies on community contributions. You are welcome to participate by submitting bug reports or feature requests, taking part in discussions, or proposing fixes and other code changes. Please -refer to the [contributing guidelines](CONTRIBUTING.md) if you are interested -in contributing. +refer to the [contributing guidelines](CONTRIBUTING.md) if you are interested in +contribute. ## License @@ -454,14 +359,13 @@ This project is covered by the [MIT License](LICENSE). ## Contact -For questions or suggestions regarding the code, please use the -[issue tracker][issue-tracker]. Do not hesitate to contact us via -[email][email] for any other inquiries. +For questions or suggestions regarding the code, please use the [issue tracker][issue-tracker]. Do not hesitate on contacting us via [email][email] for any other inquiries. © 2023 [Zavolab, Biozentrum, University of Basel][zavolab] [ascii-pileups]: [bed-format]: +[bedtools]: [chrMap]: [conda]: [cluster execution]: @@ -471,7 +375,9 @@ For questions or suggestions regarding the code, please use the [mamba]: [miniconda-installation]: [mirbase]: +[oligomap]: [rule-graph]: images/rule_graph.svg +[segemehl]: [singularity]: [slurm]: [snakemake]: From e1643cab73a33bfe765c73090144beadec68f398 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:20:55 +0200 Subject: [PATCH 29/42] revert: undo documentation branch merge --- pipeline_documentation.md | 978 +++++++++++--------------------------- 1 file changed, 266 insertions(+), 712 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index 6332027..2e2ba72 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -87,6 +87,7 @@ on installation and usage please see [here](README.md). - [`create_per_condition_ascii_pileups`](#create_per_condition_ascii_pileups) + ## Third-party software used > Tag lines were taken from the developers' websites (code repository or manual) @@ -94,26 +95,25 @@ on installation and usage please see [here](README.md). | Name | License | Tag line | More info | | --- | --- | --- | --- | | **ASCII-style alignment pileups** | [Apache 2.0][license-apache2] | _"Generates ASCII-style pileups of read alignments in one or more BAM files for one or more genomic regions."_ | [code][code-ascii] | -| **BEDTools** | [GPLv2][license-gpl2] | _"[...] intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF"_ | [code][code-bedtools] / [manual][docs-bedtools] / [publication][pub-bedtools] | +| **BEDTools** | [GPLv2][license-gpl2] | _"[...] intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF"_ | [code][code-bedtools] / [manual][manual-bedtools] / [publication][pub-bedtools] | | **cufflinks** | [BSL-1.0][license-bsl1] | _"[...] assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples"_ | [code][code-cufflinks] / [manual][docs-cufflinks] / [publication][pub-cufflinks] | | **cutadapt** | [MIT][license-mit] | _"[...] finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads"_ | [code][code-cutadapt] / [manual][docs-cutadapt] / [publication][pub-cutadapt] | | **FASTX-Toolkit** | [AGPL-3.0][license-agpl3] | _"[...] collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing"_ | [code][code-fastx] / [manual][docs-fastx] | -| **GFFUtils** | [AFL-3][license-afl3] | _"[...] a small set of utility programs for working with GFF and GTF files"_ | [code][code-gffutils] / [manual][docs-gffutils] | +| **GFFUtils** | [AFL-3][license-afl3] | _"[...] a small set of utility programs for working with GFF and GTF files"_ | [code][code-gffutils] / [manual][docs-gffutils] | | **Oligomap** | [GPLv3][license-gpl3] | _"[...] fast identification of nearly-perfect matches of small RNAs in sequence databases. It allows to exhaustively identify all the perfect and 1-error (where an error is defined to be a mismatch, insertion or deletion) matches of large sets of small RNAs to target sequences"_ | [code][code-oligomap] / [publication][pub-oligomap] | | **SAMtools** | [MIT][license-mit] | _"[...] suite of programs for interacting with high-throughput sequencing data"_ | [code][code-samtools] / [manual][docs-samtools] / [publication][pub-samtools] | -| **segemehl** | [GPLv3][license-gpl3] | _"[...] map short sequencer reads to reference genomes"_ | [manual][docs-segemehl] / [publication][pub-segemehl] | +| **segemehl** | [GPLv3][license-gpl3] | _"[...] map short sequencer reads to reference genomes"_ | [manual][docs-segemehl] / [publication][pub-segemehl] | ## Description of workflow steps -> The workflow consists of five Snakemake files: A main `Snakefile` and an -> individual Snakemake file each for the genome resources preparation, the -> reads mapping, the miRNA quantification and the ASCII-style pileups -> generation. The main `Snakefile` contains the configuration file validation -> and imports the various functional modules described below. Individual steps -> of the workflow are described briefly along with some examples, and links to -> the respective software manuals are given. Parameters that can be modified by -> the user (via the samples table and the configuration file) are also -> described. +> The workflow consists of four Snakemake files: A main `Snakefile` and an +individual Snakemake file for each step in the workflow (the file preparation, +the reads mapping, the miRNA quantification and the ASCII-style alignment +pileups generation). The main `Snakefile` contains the configuration file +validation along with the inclusion of the sub-workflows. Individual steps of +the workflow are described briefly, and links to the respective software +manuals are given. Parameters that can be modified by the user (via the samples +table and the configuration file) are also described. ### Rule graph @@ -128,17 +128,17 @@ Visual representation of the workflow. Automatically prepared with ##### Requirements -- Tab-separated values (`.tsv`) file +- tab-separated values (`.tsv`) file - First row has to contain parameter names as in [`samples_table.tsv`](test/test_files/samples_table.tsv) - First column used as sample identifiers Parameter name | Description | Data type(s) --- | --- | --- -sample | Arbitrary name for the miRNA sequence library. | `str` -sample_file | Path to the `gzip`ped miRNA sequencing library file. The path must be relative to the directory where the workflow will be run. | `str` -adapter | Sequence of the 3'-end adapter used during library preparation. Required for [Cutadapt](#third-party-software-used). Use a value such as `XXXXXXXXXX` if no adapter is present or if no trimming is desired. | `str` -format | One of `fa`/`fasta` or `fq`/`fastq`, if the library file is in FASTA or FASTQ format, respectively. | `str` +sample | Descriptive sample name. | `str` +sample_file | Path of the library file in either `.fa.gz` or `.fastq.gz` format. | `str` +adapter | Required for [Cutadapt](#third-party-software-used). Use a value such as `XXXXXXXXXX` if no adapter is present or if no trimming is desired | `str` +format | There are two allowed values, `fa` and `fastq` according to the library format | `str` #### Configuration file @@ -147,7 +147,6 @@ Some parameters within the workflow can be modified. Refer to the [configuration template](#config/config_template.yaml) for a detailed explanation of each option. - ### Snakefile #### `finish` @@ -157,17 +156,19 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - (**Workflow output**) SAM file with the pri-miR intersecting alignments; - from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - - (**Workflow output**) SAM file with the mature miRNA intersecting alignments; from - [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - - (**Workflow output**) (iso)miR and/or pri-miR counts table (`.tab`); from + - pri-miR intersections file (`.bed`); from + [**intersect_extended_primir**](#intersect_extended_primir) + - miRNA intersections file (`.bed`); from + [**intersect_extended_mirna**](#intersect_extended_mirna) + - Alignments file, sorted and tagged (`.sam`); from + [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) + - (iso)miR and/or pri-miR counts table (`.tab`); from [**merge_tables**](#merge_tables) - - (**Workflow output**) BAM file with the contributing alignments, sorted; - from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - (**Workflow output**) BAM index file (`.bam.bai`); from + - Alignments file (`.bam`); from + [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) + - `BAM` index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - - (**Workflow output**) Empty text file (`.txt`) + - Empty text file (`.txt`); from [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -188,13 +189,13 @@ Target rule as required by [Snakemake][docs-snakemake]. [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome) - Exon annotations (`.bed`); from [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) - - SAM header (`.sam`); from + - Genome header (`.sam`); from [**create_genome_header**](#create_genome_header) - Tab-separated table mapping chromosome name(s) and length(s) (`.tsv`); from [**extract_chr_len**](#extract_chr_len) - - Primary miRNA transcript (pri-miR) extended annotations (`.gff3`); + - Primary miRNA transcript (pri-miR) extended annotation (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) - - Mature miRNA (miRNA) extended annotations (`.gff3`); + - Mature miRNA (miRNA) extended annotation (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) @@ -203,9 +204,9 @@ Target rule as required by [Snakemake][docs-snakemake]. Trim genome sequence IDs with a [**custom script**][custom-script-trim-id]. - **Input** - - (**Workflow input**) Genome sequence, `gzip`ed (`.fa.gz`/`.fasta.gz`) + - Genome sequence file (`.fasta`) - **Output** - - Genome sequence, trimmed IDs (`.fa`); used in + - Genome sequence file, trimmed IDs (`.fasta`); used in [**extract_transcriptome_seqs**](#extract_transcriptome_seqs), [**create_genome_header**](#create_genome_header), [**create_index_genome_fasta**](#create_index_genome), @@ -217,28 +218,25 @@ Trim genome sequence IDs with a [**custom script**][custom-script-trim-id]. #### `extract_transcriptome_seqs` -Create transcriptome from genomic sequence and annotations with +Create transcriptome from genome and genome annotations with [**cufflinks**](#third-party-software-used). - **Input** - - (**Workflow input**) Genome annotations, `gzip`ed (`.gtf.gz`) - - Genome sequence, trimmed IDs (`.fa`); from - [**trim_genome_seq_ids**](#trim_genome_seq_ids) + - Genome sequence file (`.fasta`) + - Genome annotation file (.`gtf`) - **Output** - - Transcriptome sequence (`.fa`); used in + - Transcriptome sequence file (`.fasta`); used in [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) #### `trim_transcriptome_seq_ids` -Trim transcriptome sequence IDs with a -[**custom script**][custom-script-trim-id]. +Trim transcriptome sequence IDs with a [**custom script**][custom-script-trim-id]. - **Input** - - Transcriptome sequence (`.fa`); from - [**extract_transcriptome_seqs**](#extract_transcriptome_seqs) + - Transcriptome sequence file (`.fasta`) - **Output** - - Transcriptome sequence, trimmed IDs (`.fa`); used in + - Transcriptome sequence, trimmed IDs (`.fasta`); used in [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome), [**mapping_transcriptome_segemehl**](#mapping_transcriptome_segemehl) and [**mapping_transcriptome_oligomap**](#mapping_transcriptome_oligomap) @@ -250,14 +248,14 @@ Generate transcriptome index for [**segemehl**](#third-party-software-used) short read aligner. > The transcriptome index only needs to be generated once for each combination -> of transcriptome sequence and annotations, and sample sets. +of genome and annotations and sample sets. - **Input** - - Transcriptome sequence, trimmed IDs (`.fa`); from + - Transcriptome sequence file, trimmed IDs (`.fasta`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - **Output** - segemehl transcriptome index (`.idx`); used in - [**mapping_transcriptome_segemehl**](#mapping_transcriptome_segemehl) + [**mapping_genome_segemehl**](#mapping_genome_segemehl) #### `generate_segemehl_index_genome` @@ -266,10 +264,10 @@ Generate genome index for [**segemehl**](#third-party-software-used) short read aligner. > The genome index only needs to be generated once for each combination -> of annotations and sample sets. +of annotations and sample sets. - **Input** - - Genome sequence, trimmed IDs (`.fa`); from + - Genome sequence file with trim IDs (`.fasta`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - segemehl genome index (`.idx`); used in @@ -282,12 +280,11 @@ Retrieve exon annotations from genome annotations with a [**custom script**][custom-script-get-lines]. - **Input** - - (**Workflow input**) Genome annotations, `gzip`ed (`.gtf.gz`) + - Genomic annotations (`.gtf`) - **Output** - Exon annotations (`.gtf`); used in [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) - #### `convert_exons_gtf_to_bed` Convert exon annotations `.gtf` to `.bed` with a @@ -302,33 +299,33 @@ Convert exon annotations `.gtf` to `.bed` with a #### `create_genome_header` -Create SAM header for the genome with +Create `SAM` header for the genome with [**SAMtools**](#third-party-software-used). -> Required by [SAMtools](#third-party-software-used) to work with the -> alignment files. +> Required by [SAMtools](#third-party-software-used) to work with the alignment +file. - **Input** - - Genome sequence, trimmed IDs (`.fa`); from + - Genome sequence file, trimmed IDs (`.fasta`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - SAM genome header (`.sam`); used in - [add_header_all_maps](#add_header_all_maps) + - Genome header (`.sam`); used in [add_header_all_maps](#add_header_all_maps) #### `map_chr_names` -Map UCSC-like chromosome names with Ensembl-like ones in miRNA annotations +Map UCSC-like chromosome names with Ensembl-like ones in miRNA annotation with a [**custom script**][custom-script-map-chr]. > Required by [BEDTools](#third-party-software) to intersect alignments with -> miRNA annotations. Several mapping tables are available [here][chr-maps]. +miRNA annotations. Several mapping tables are available [here][chr-maps]. - **Input** - - (**Workflow input**) miRNA annotations (`.gff3`) - - (**Workflow input**) Tab-separated chromosome name mappings table (`.tsv`) + - miRNA annotations (`.gff3`) + - Tab-separated mappings table (`.tsv`) - **Output** - - miRNA annotations, mapped chromosome name(s) (`.gff3`); used in + - miRNA annotations with mapped genes(`.gff3`); used in + [**extend_mirs_annotations**](#extend_mirs_annotations), [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -336,14 +333,14 @@ with a [**custom script**][custom-script-map-chr]. #### `create_index_genome_fasta` -Create a FASTA index for the genome with +Create a `FASTA` index for the genome with [**SAMtools**](#third-party-software-used). - **Input** - - Genome sequence, trimmed IDs (`.fa`); from + - Genome sequence file, trimmed IDs (`.fasta`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - FASTA genome index (`.fa.fai`); used in + - `FASTA` genome index (`.fa.fai`); used in [**extract_chr_len**](#extract_chr_len) @@ -351,12 +348,8 @@ Create a FASTA index for the genome with Extract chromosome(s) length from the genome sequence. -> Required to ensure that the extended annotations in generated in the -> [**extend_mirs_annotations**](#extend_mirs_annotations) rule do not exceed -> the chromosome(s) boundaries. - - **Input** - - FASTA genome index (`.fa.fai`); from + - `FASTA` genome index (`.fa.fai`); from [**create_index_genome_fasta**](#create_index_genome_fasta) - **Output** - Tab-separated table mapping chromosome name(s) and length(s) (`.tsv`); used @@ -365,148 +358,25 @@ Extract chromosome(s) length from the genome sequence. #### `extend_mirs_annotations` -Extend miRNA annotations, ensure feature names uniqueness and split the file -by feature with a [**custom script**][custom-script-mir-ext]. - -> Adjust miRNAs' 'Name' attribute to account for the different genomic -> locations the miRNA sequence is annotated on and ensure their uniqueness. -> The name format is `SPECIES-mir-NAME-#` for pri-miRs, and -> `SPECIES-miR-NAME-#-ARM` or `SPECIES-miR-NAME-#` for mature miRNA with both -> or just one arm respectively, where `#` is the replica integer. If a pri-miR -> has a replica but its number is set in the 'ID' attribute, the first instance -> does not has a suffix but the other one(s) do. If a precursor has no other -> occurrences, no further modifications are made. On the other hand, -> mature miRNA regions are extended on both sides to account for isomiR species -> with shifted start and/or end positions without exceeding chromosome(s) -> boundaries. If required, pri-miR loci are also extended to accommodate the -> new miRNA coordinates. In addition, pri-miR names are modified to record the -> final positions by appending `_-y` and `_+x` to them, where `y` is the 5' -> shift and `x` the 3' shift. - -- **Input** - - miRNA annotations, mapped chromosome name(s) (`.gff3`); from +Extend miRNA annotations and split the file by feature with a +[**custom script**][custom-script-mir-ext]. + +> Mature miRNA regions are extended on both sides to account for isomiR species +with shifted start and/or end positions. If required, pri-miR loci are also +extended to accommodate the new miRNA coordinates. + +- **Input** + - miRNA annotations with mapped chromosomes(`.gff3`); from [**map_chr_names**](#map_chr_names) - **Parameters** - **config_template.yaml** - `extension`: Number of nucleotides by which mature miRNA annotated - regions are extended at most (default: 6) + regions are extended (default 6) - **Output** - - Primary miRNA transcript (pri-miR) extended annotations (`.gff3`); used in + - Primary miRNA transcript (pri-miR) extended annotation (`.gff3`); used in [**intersect_extended_primir**](#intersect_extended_primir) - - Mature miRNA (miRNA) extended annotations (`.gff3`); used in + - Mature miRNA (miRNA) extended annotation (`.gff3`); used in [**intersect_extended_mirna**](#intersect_extended_mirna) -- **Examples** - -```console -Example 1 | Extension | Mature miRNA extension - -IN: - pri-miR entry: - 19 . miRNA_primary_transcript 2517 2614 . + . ID=MI0003141;Alias=MI0003141;Name=hsa-mir-512-2 - mature miRNA entry: - 19 . miRNA 2536 2558 . + . ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003141 - extension: - 6 -OUT: - pri-miR entry: - 19 . miRNA_primary_transcript 2517 2614 . + . ID=MI0003141;Alias=MI0003141;Name=hsa-mir-512-2_-0_+0 - mature miRNA entry: - 19 . miRNA 2530 2564 . + . ID=MIMAT0002822_1;Alias=MIMAT0002822;Name=hsa-miR-512-2-5p;Derives_from=MI0003141 - - -Example 2 | Extension | Mature miRNA and pri-miR extension - -IN: - pri-miR entry: - 19 . miRNA_primary_transcript 9 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1 - mature miRNA entry: - 19 . miRNA 12 74 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 - extension: - 6 -OUT: - pri-miR entry: - 19 . miRNA_primary_transcript 6 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-3_+0 - mature miRNA entry: - 19 . miRNA 6 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-1-5p;Derives_from=MI0003140 - - -Example 3 | Extension | Matrue miRNA exceeding chromosome boundaries extension - -IN: - pri-miR entry: - 19 . miRNA_primary_transcript 2 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1 - mature miRNA entry: - 19 . miRNA 3 74 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-5p;Derives_from=MI0003140 - extension: - 6 -OUT: - pri-miR entry: - 19 . miRNA_primary_transcript 1 122 . + . ID=MI0003140;Alias=MI0003140;Name=hsa-mir-512-1_-1_+0 - mature miRNA entry: - 19 . miRNA 1 80 . + . ID=MIMAT0002822;Alias=MIMAT0002822;Name=hsa-miR-512-1-5p;Derives_from=MI0003140 - - -Example 4 | Name uniqueness | Replica number in the ID - -IN: - pri-miR entries: - chr21 . miRNA_primary_transcript 8206563 8206618 . + . ID=MI0033425;Alias=MI0033425;Name=hsa-mir-10401 - chr21 . miRNA_primary_transcript 8250772 8250827 . + . ID=MI0033425_2;Alias=MI0033425;Name=hsa-mir-10401 - mature miRNA entries: - chr21 . miRNA 8206563 8206582 . + . ID=MIMAT0041633;Alias=MIMAT0041633;Name=hsa-miR-10401-5p;Derives_from=MI0033425 - chr21 . miRNA 8206598 8206618 . + . ID=MIMAT0041634;Alias=MIMAT0041634;Name=hsa-miR-10401-3p;Derives_from=MI0033425 - chr21 . miRNA 8250772 8250791 . + . ID=MIMAT0041633_1;Alias=MIMAT0041633;Name=hsa-miR-10401-5p;Derives_from=MI0033425 - chr21 . miRNA 8250807 8250827 . + . ID=MIMAT0041634_1;Alias=MIMAT0041634;Name=hsa-miR-10401-3p;Derives_from=MI0033425 -OUT: - pri-miR entries: - chr21 . miRNA_primary_transcript 8206563 8206618 . + . ID=MI0033425;Alias=MI0033425;Name=hsa-mir-10401 - chr21 . miRNA_primary_transcript 8250772 8250827 . + . ID=MI0033425_2;Alias=MI0033425;Name=hsa-mir-10401-2 - mature miRNA entries: - chr21 . miRNA 8206563 8206582 . + . ID=MIMAT0041633;Alias=MIMAT0041633;Name=hsa-miR-10401-5p;Derives_from=MI0033425 - chr21 . miRNA 8206598 8206618 . + . ID=MIMAT0041634;Alias=MIMAT0041634;Name=hsa-miR-10401-3p;Derives_from=MI0033425 - chr21 . miRNA 8250772 8250791 . + . ID=MIMAT0041633_1;Alias=MIMAT0041633;Name=hsa-miR-10401-2-5p;Derives_from=MI0033425 - chr21 . miRNA 8250807 8250827 . + . ID=MIMAT0041634_1;Alias=MIMAT0041634;Name=hsa-miR-10401-2-3p;Derives_from=MI0033425 - - -Example 5 | Name uniqueness | Replica number in the Name; single mature arm - -IN: - pri-miR entries: - chr21 . miRNA_primary_transcript 8205315 8205406 . + . ID=MI0022559;Alias=MI0022559;Name=hsa-mir-6724-1 - chr21 . miRNA_primary_transcript 8249505 8249596 . + . ID=MI0031516;Alias=MI0031516;Name=hsa-mir-6724-2 - mature miRNA entries: - chr21 . miRNA 8205325 8205347 . + . ID=MIMAT0025856;Alias=MIMAT0025856;Name=hsa-miR-6724-5p;Derives_from=MI0022559 - chr21 . miRNA 8249515 8249537 . + . ID=MIMAT0025856_1;Alias=MIMAT0025856;Name=hsa-miR-6724-5p;Derives_from=MI0031516 -OUT: - pri-miR entries: - chr21 . miRNA_primary_transcript 8205315 8205406 . + . ID=MI0022559;Alias=MI0022559;Name=hsa-mir-6724-1 - chr21 . miRNA_primary_transcript 8249505 8249596 . + . ID=MI0031516;Alias=MI0031516;Name=hsa-mir-6724-2 - mature miRNA entries: - chr21 . miRNA 8205325 8205347 . + . ID=MIMAT0025856;Alias=MIMAT0025856;Name=hsa-miR-6724-1-5p;Derives_from=MI0022559 - chr21 . miRNA 8249515 8249537 . + . ID=MIMAT0025856_1;Alias=MIMAT0025856;Name=hsa-miR-6724-2-5p;Derives_from=MI0031516 - - -Example 6 | Name uniqueness | Both mature miRNA arms but just one with the replica number - -IN: - pri-miR entries: - chr2 . miRNA_primary_transcript 135665397 135665478 . + . ID=MI0000447;Alias=MI0000447;Name=hsa-mir-128-1 - chr3 . miRNA_primary_transcript 35744476 35744559 . + . ID=MI0000727;Alias=MI0000727;Name=hsa-mir-128-2 - mature miRNA entries: - chr2 . miRNA 135665446 135665466 . + . ID=MIMAT0000424;Alias=MIMAT0000424;Name=hsa-miR-128-3p;Derives_from=MI0000447 - chr2 . miRNA 135665411 135665433 . + . ID=MIMAT0026477;Alias=MIMAT0026477;Name=hsa-miR-128-1-5p;Derives_from=MI0000447 - chr3 . miRNA 35744527 35744547 . + . ID=MIMAT0000424_1;Alias=MIMAT0000424;Name=hsa-miR-128-3p;Derives_from=MI0000727 - chr3 . miRNA 35744490 35744512 . + . ID=MIMAT0031095;Alias=MIMAT0031095;Name=hsa-miR-128-2-5p;Derives_from=MI0000727 -OUT: - pri-miR entries: - chr2 . miRNA_primary_transcript 135665397 135665478 . + . ID=MI0000447;Alias=MI0000447;Name=hsa-mir-128-1 - chr3 . miRNA_primary_transcript 35744476 35744559 . + . ID=MI0000727;Alias=MI0000727;Name=hsa-mir-128-2 - mature miRNA entries: - chr2 . miRNA 135665446 135665466 . + . ID=MIMAT0000424;Alias=MIMAT0000424;Name=hsa-miR-128-1-3p;Derives_from=MI0000447 - chr2 . miRNA 135665411 135665433 . + . ID=MIMAT0026477;Alias=MIMAT0026477;Name=hsa-miR-128-1-5p;Derives_from=MI0000447 - chr3 . miRNA 35744527 35744547 . + . ID=MIMAT0000424_1;Alias=MIMAT0000424;Name=hsa-miR-128-2-3p;Derives_from=MI0000727 - chr3 . miRNA 35744490 35744512 . + . ID=MIMAT0031095;Alias=MIMAT0031095;Name=hsa-miR-128-2-5p;Derives_from=MI0000727 -``` ### Map workflow @@ -517,94 +387,89 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - BAM index file (`.bam.bai`); from + - `BAM` index file (`.bam.bai`); from [**index_all_alns_bam**](#index_all_alns_bam) + #### `start` Copy and rename read files. > Local rule. -> Depending on the library file format, the output file undergoes a quality -> filter (`fa`/`.fastq`) or is directly formatted (`.fa`/`.fasta`). +Depending on the read files format, the output files undergo a quality filter +(`.fastq`) or are directly formatted (`.fa`). - **Input** - - (**Workflow input**) miRNA sequencing library, `gzip`ed - (`.fa.gz`/`.fasta.gz` or `.fq.gz`/`.fastq.gz`) + - Reads file (`.fa.gz`, `.fastq.gz`) - **Output** - - miRNA sequencing library, copied, renamed (`.fa`, `.fastq`); used in - [**fastq_quality_filter**](#fastq_quality_filter) and/or + - Reads file, copied, renamed (`.fa`, `.fastq`); used in + [**fastq_quality_filter**](#fastq_quality_filter) or [**format_fasta**](#format_fasta) #### `fastq_quality_filter` -Conduct quality control for reads library with +Conduct quality control for reads library with [**fastx_toolkit**](#third-party-software-used). - **Input** - - miRNA sequencing library, copied, renamed (`.fastq`); from - [**start**](#start) + - Reads file, copied, renamed (`.fastq`); from [**start**](#start) - **Parameters** - **config_template.yaml** - - `q_value`: Minimum Q (Phred) score to keep (default: 10) + - `q_value`: Minimum Q (Phred) score to keep (default 10) - `p_value`: Minimum % of bases that must have a Q (Phred) quality - (default: 50) + (default 50) - **Output** - - miRNA sequencing library, filtered (`.fastq`); used in + - Reads file, filtered (`.fastq`); used in [**fastq_to_fasta**](#fastq_to_fasta) #### `fastq_to_fasta` -Convert reads file from FASTQ to FASTA with +Convert reads file from `.fastq` to `.fa` with [**fastx_toolkit**](#third-party-software-used). -> Sequence identifiers are renamed to numbers. - - **Input** - - miRNA sequencing library, filtered (`.fastq`); from + - Reads file, filtered (`.fastq`); from [**fastq_quality_filter**](#fastq-quality-filter) - **Output** - - miRNA sequencing library (`.fa`); used in [**format_fasta**](#format_fasta) - + - Reads file (`.fa`); used in [**format_fasta**](#format_fasta) #### `format_fasta` -Format read's sequences to appear on a single line with +Format reads to appear on a single line with [**fastx_toolkit**](#third-party-software-used). - **Input** - - miRNA sequencing library (`.fa`); from [**start**](#start) or + - Reads file (`.fa`); from [**start**](#start) or [**fastq_to_fasta**](#fastq_to_fasta) - **Output** - - miRNA sequencing library, formatted (`.fasta`); used in + - Reads file, formatted (`.fa`); used in [**remove_adapters**](#remove_adapters) #### `remove_adapters` -Trim 3' adapters and `N` bases at either end. Filter reads by minimum length -and number of inner `N` bases with [**cutadapt**](#third-party-software-used). +Trim adapters and `N` bases at either end. Filter reads by minimum length and +number of inner `N` bases with [**cutadapt**](#third-party-software-used). - **Input** - - miRNA sequencing library, formatted (`.fasta`); from - [**format_fasta**](#format_fasta) + - Reads file (`.fa`); from [**format_fasta**](#format_fasta) - **Parameters** - **samples.tsv** - - Adapter to be removed; specified in the sample's table column `adapter` + - Adapter to be removed; specify in sample table column `adapter` - **config_template.yaml** - `error_rate`: Fraction of allowed errors in the matched adapters - (default: 0.1) + (default 0.1) - `overlap`: Minimum overlap length between adapter and read to trim the - bases (default: 3) + bases (default 3) - `minimum_length`: Minimum length for a processed read to be kept - (default: 15) - - `max_n`: Maximum number of inner `N` bases for a processed read to be - kept (default: 0) + (default 15) + - `max_n`: Maximum number of `N` bases for a processed read to be kept + (default 0) - **Output** - - miRNA sequencing library, filtered, without adapters (`.fasta`); used in + - Reads file (`.fa`; used in [**collapse_identical_reads**](#collapse_identical_reads) @@ -613,15 +478,10 @@ and number of inner `N` bases with [**cutadapt**](#third-party-software-used). Collapse and rename identical reads [**fastx_toolkit**](#third-party-software-used). -> Sequences are renamed in the format `R-N`, where `R` is the assigned number -> to the unique entry, and `N` is the amount of identical sequences within the -> library collapsed in it. - - **Input** - - miRNA sequencing library, filtered, without adapters (`.fasta`); from - [**remove_adapters**](#remove_adapters) + - Reads file (`.fa`); from [**remove_adapters**](#remove_adapters) - **Output** - - miRNA sequencing library, collapsed, renamed (`.fasta`); used in + - Reads file, collapsed, rename; used in [**filter_fasta_for_oligomap**](#filter_fasta_for_oligomap), [**map_genome_segemehl**](#map_genome_segemehl) and [**map_transcriptome_segemehl**](#map_transcriptome_segemehl) @@ -633,11 +493,11 @@ Align short reads to reference genome with [**segemehl**](#third-party-software-used). - **Input** - - miRNA sequencing library, collapsed, renamed (`.fasta`); from + - Reads file, collapsed (`.fa`); from [**collapse_identical_reads**](#collapse_identical_reads) - - Genome sequence, trimmed IDs (`.fa`); from + - Genome sequence (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - - segemehl genome index (`.idx`); from + - segemehl genome index (`idx`); from [**generate_segemehl_index_genome**](#generate_segemehl_index_genome) - **Output** - Alignments file (`.sam`); used in @@ -650,11 +510,11 @@ Align short reads to reference transcriptome with [**segemehl**](#third-party-software-used). - **Input** - - miRNA sequencing library, collapsed, renamed (`.fasta`); from + - Reads file, collapsed (`.fa`); from [**collapse_identical_reads**](#collapse_identical_reads) - - Transcriptome sequence, trimmed IDs (`.fa`); from + - Transcriptome sequence (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - - segemehl transcriptome index (`.idx`); from + - segemehl transcriptome index (`idx`); from [**generate_segemehl_index_transcriptome**](#generate_segemehl_index_transcriptome) - **Output** - Alignments file (`.sam`); used in @@ -665,21 +525,16 @@ Align short reads to reference transcriptome with Filter reads by length with a [**custom script**][custom-script-validation]. -> Required for an optimal mapping speed. Oligomap is specifically written for -> short reads. Therefore, reads with more bases than the default maximum (30 -> nts) makes the mapping slower. - - **Input** - - miRNA sequencing library, collapsed, renamed (`.fasta`); from + - Reads file, collapsed (`.fa`); from [**collapse_identical_reads**](#collapse_identical_reads) - **Parameters** - **config_template.yaml** - - `max_length_reads`: Maximum length of processed reads to be mapped with - [**oligomap**](#third-party-software-used) (default: 30) + - `max_length_reads`: Maximum length of processed reads to map with + [**oligomap**](#third-party-software-used) - **Output** - - miRNA sequencing library, collapsed, filtered (`.fasta`); used in - [**map_genome_oligomap**](#map_genome_oligomap) and - [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) + - Reads file (`.fa`); used in [**map_genome_oligomap**](#map_genome_oligomap) + and [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) #### `map_genome_oligomap` @@ -687,18 +542,16 @@ Filter reads by length with a [**custom script**][custom-script-validation]. Align short reads to reference genome with [**oligomap**](#third-party-software-used). -> Refer to Oligomap's [**Output format section**][oligomap-out] for a specific -> explanation and examples on the output format. - - **Input** - - miRNA sequencing library, collapsed, filtered (`.fasta`); from + - Reads file, collapsed (`.fa`); from [**filter_fasta_for_oligomap**](#filter_fasta_for_oligomap) - - Genome sequence, trimmed IDs (`.fa`); from + - Genome sequence (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - Alignments file (`.oligomap`); used in + - Alignments file (`.fa`); used in + [**sort_genome_oligomap**](#sort_genome_oligomap) + - Alignment report (`.txt`); used in [**sort_genome_oligomap**](#sort_genome_oligomap) - - Alignments report (`.txt`) #### `sort_genome_oligomap` @@ -707,33 +560,32 @@ Sort [**oligomap**](#third-party-software-used) alignments by query name with a [**custom script**][custom-script-blocksort]. - **Input** - - Alignments file (`.oligomap`); from + - Alignments file (`.fa`); from + [**map_genome_oligomap**](#map_genome_oligomap) + - Alignment report (`.txt`); from [**map_genome_oligomap**](#map_genome_oligomap) - **Output** - - Alignments file, sorted (`.oligomap`); used in + - Alignments file, sorted (`.fa`); used in + [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) + - Alignment report, sorted (`.txt`); used in [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) #### `convert_genome_to_sam_oligomap` -Convert aligned reads `.oligomap` to `.sam` and filter alignments by number of -hits with a [**custom script**][custom-script-oligo-sam]. - -> If a read has been aligned beyond a specified threshold, it is removed due -> to (1) performance reasons as the file size can rapidly increase, and (2) -> the fact that each read contributes to each count `1/N` where `N` is the -> number of genomic loci it aligns to and a large `N` makes the contribution -> negligible. +Convert aligned reads `.fa` to `.sam` and filter alignments by number of hits +with a [**custom script**][custom-script-oligo-sam]. - **Input** - - Alignments file, sorted (`.oligomap`); from + - Alignments file, sorted (`.fa`); from + [**sort_genome_oligomap**](#sort_genome_oligomap) + - Alignment report, sorted (`.txt`); from [**sort_genome_oligomap**](#sort_genome_oligomap) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of mappings per read to be kept (default: 100) + - `nh`: Maximum number of hits an alignment can have to be kept - **Output** - - Alignments file, filtered (`.sam`); used in - [**merge_genome_maps**](#merge_genome_maps) + - Alignments file (`.sam`); used in [**merge_genome_maps**](#merge_genome_maps) #### `map_transcriptome_oligomap` @@ -741,18 +593,16 @@ hits with a [**custom script**][custom-script-oligo-sam]. Align short reads to reference transcriptome with [**oligomap**](#third-party-software-used). -> Refer to Oligomap's [Output format section][oligomap-out] for a specific -> explanation and examples on the output format. - - **Input** - - miRNA sequencing library, collapsed, filtered (`.fasta`); from + - Reads file (`.fa`); from [**filter_fasta_for_oligomap**](#filter_fasta_for_oligomap) - - Transcriptome sequence, trimmed IDs (`.fa`); from + - Transcriptome sequence (`.fa`); from [**trim_transcriptome_seq_ids**](#trim_transcriptome_seq_ids) - **Output** - - Alignments file (`.oligomap`); used in + - Alignments file (`.fa`); used in + [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) + - Alignment report (`.txt`); used in [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - - Alignments report (`.txt`) #### `sort_transcriptome_oligomap` @@ -761,32 +611,32 @@ Sort [**oligomap**](#third-party-software-used) alignments by query name with a [**custom script**][custom-script-blocksort]. - **Input** - - Alignments file (`.oligomap`); from + - Alignments file (`.fa`); from + [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) + - Alignment report (`.txt`); from [**map_transcriptome_oligomap**](#map_transcriptome_oligomap) - **Output** - - Alignments file, sorted (`.oligomap`); used in + - Aligned file, sorted (`.fa`); used in [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptome_to_sam_oligomap) + - Alignment report, sorted (`.txt`); used in + [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptme_to_sam_oligomap) #### `convert_transcriptome_to_sam_oligomap` -Convert aligned reads `.oligomap` to `.sam` and filter alignments by number of -hits with a [**custom script**][custom-script-oligo-sam]. - -> If a read has been aligned beyond a specified threshold, it is removed due -> to (1) performance reasons as the file size can rapidly increase, and (2) -> the fact that each read contributes to each count `1/N` where `N` is the -> number of genomic loci it aligns to and a large `N` makes the contribution -> negligible. +Convert aligned reads `.fa` to `.sam` and filter alignments by number of hits +with a [**custom script**][custom-script-oligo-sam]. - **Input** - - Alignments file, sorted (`.oligomap`); from + - Alignments file, sorted (`.fa`); from + [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) + - Alignment report, sorted (`.txt`); from [**sort_transcriptome_oligomap**](#sort_transcriptome_oligomap) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of mappings per read to be kept (default: 100) + - `nh`: Maximum number of hits an alignment can have to be kept - **Output** - - Alignments file, filtered (`.sam`); used in + - Alignments file (`.sam`); used in [**merge_transcriptome_maps**](#merge_transcriptome_maps) @@ -798,7 +648,7 @@ Concatenate [**segemehl**](#third-party-software-used) and - **Input** - Alignments file (`.sam`); from [**map_genome_segemehl**](#map_genome_segemehl) - - Alignments file, filtered (`.sam`); from + - Alignments file (`.sam`); from [**convert_genome_to_sam_oligomap**](#convert_genome_to_sam_oligomap) - **Output** - Alignments file (`.sam`); used in @@ -813,7 +663,7 @@ Concatenate [**segemehl**](#third-party-software-used) and - **Input** - Alignments file (`.sam`); from [**map_transcriptome_segemehl**](#map_transcriptome_segemehl) - - Alignments file, filtered (`.sam`); from + - Alignments file (`.sam`); from [**convert_transcriptome_to_sam_oligomap**](#convert_transcriptome_to_sam_oligomap) - **Output** - Alignments file (`.sam`); used in @@ -825,40 +675,27 @@ Concatenate [**segemehl**](#third-party-software-used) and Filter merged genome alignments by the number of hits with a [**custom script**][custom-script-nh-filter]. -> If a read has been aligned beyond a specified threshold, it is removed due -> to (1) performance reasons as the file size can rapidly increase, and (2) -> the fact that each read contributes to each count `1/N` where `N` is the -> number of genomic loci it aligns to and a large `N` makes the contribution -> negligible. - - **Input** - Alignments file (`.sam`); from [**merge_genome_maps**](#merge_genome_maps) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of mappings per read to be kept (default: 100) + - `nh`: Maximum number of mappings per read to be kept (default 100) - **Output** - Alignments file, filtered (`.sam`); used in [**remove_header_genome_mappings**](#remove_header_genome_mappings) - #### `filter_transcriptome_by_nh` Filter merged transcriptome alignments by the number of hits with a [**custom script**][custom-script-nh-filter]. -> If a read has been aligned beyond a specified threshold, it is removed due -> to (1) performance reasons as the file size can rapidly increase, and (2) -> the fact that each read contributes to each count `1/N` where `N` is the -> number of genomic loci it aligns to and a large `N` makes the contribution -> negligible. - - **Input** - Alignments file (`.sam`); from [**merge_transcriptome_maps**](#merge_transcriptme_maps) - **Parameters** - **config_template.yaml** - - `nh`: Maximum number of mappings per read to be kept (default: 100) + - `nh`: Maximum number of mappings per read to be kept (default 100) - **Output** - Alignments file, filtered (`.sam`); used in [**remove_header_transcriptome_mappings**](#remove_header_transcriptome_mappings) @@ -866,66 +703,63 @@ Filter merged transcriptome alignments by the number of hits with a #### `remove_header_genome_mappings` -Remove the SAM header of the genome alignments file with +Remove the `SAM` header of the genome alignments file with [**SAMtools**](#third-party-software-used). - **Input** - Alignments file (`.sam`); from [**filter_genome_by_nh**](#filter_genome_by_nh) - **Output** - - Alignments file, without SAM header (`.sam`); used in - [**merge_all_maps**](#merge_all_maps) + - Alignments file (`.sam`); used in [**merge_all_maps**](#merge_all_maps) #### `remove_header_transcriptome_mappings` -Remove the SAM header of the transcriptome alignments file with +Remove the `SAM` header of the transcriptome alignments file with [**SAMtools**](#third-party-software-used). - **Input** - Alignments file (`.sam`); from [**filter_transcriptome_by_nh**](#filter_transcriptome_by_nh) - **Output** - - Alignments file, without SAM header (`.sam`); used in + - Alignments file (`.sam`); used in [**transcriptome_to_genome_maps**](#transcriptome_to_genome_maps) #### `transcriptome_to_genome_maps` -Convert the alignments' transcriptome coordinates to genomic ones with a +Convert the alignments transcriptome coordinates to genomic ones with a [**custom script**][custom-script-sam-trx]. - **Input** - - Alignments file, without SAM header (`.sam`); from + - Alignments file (`.sam`); from [**remove_header_transcriptome_mappings**](#remove_header_transcriptome_mappings) - Exon annotations (`.bed`); from [**convert_exons_gtf_to_bed**](#convert_exons_gtf_to_bed) - **Output** - - Alignments file, without SAM header (`.sam`); used in - [**merge_all_maps**](#merge_all_maps) + - Alignments file (`.sam`); used in [**merge_all_maps**](#merge_all_maps) #### `merge_all_maps` -Concatenate the four alignment files into a single one. +Concatenate the four alignments files into a single file. - **Input** - - Alignments files, without SAM header (`.sam`); from + - Alignments file (`.sam`); from [**remove_header_genome_mappings**](#remove_header_genome_mappings) and [**transcriptome_to_genome_maps**](#transcriptome_to_genome_maps) - **Output** - - Alignments file, without SAM header (`.sam`); used in + - Alignments file (`.sam`); used in [**add_header_all_maps**](#add_header_all_maps) #### `add_header_all_maps` -Add the SAM header to the aligned reads merged file with +Add the `SAM` header to the aligned reads with [**SAMtools**](#third-party-software-used). - **Input** - - Alignments file, without SAM header (`.sam`); from - [**merge_all_maps**](#merge_all_maps) + - Alignments file (`.sam`); from [**merge_all_maps**](#merge_all_maps) - **Output** - Alignments file (`.sam`); used in [**sort_maps_by_id**](#sort_maps_by_id) @@ -948,94 +782,30 @@ Remove duplicate and inferior alignments with a [**custom script**][custom-script-remove-dup]. > Alignments are considered to be duplicates if having identical entries for -> the fields `QNAME`, `FLAG`, `RNAME`, `POS` and `CIGAR`. -> Alignments are considered to be inferiors if having the same `QNAME` and -> a bigger edit distance than the smaller one within the group. The tags `NH` -> (number of hits) and `HI` (query hit index) are updated accordingly. +the fields `QNAME`, `FLAG`, `RNAME`, `POS` and `CIGAR`. +Alignments are considered to be inferiors if having the same `QNAME` and +a bigger edit distance than the minimum one within the group. + - **Input** - - Alignments file, sorted (`.sam`); from - [**sort_maps_by_id**](#sort_maps_by_id) + - Alignments file, sorted (`.sam`); from [**sort_maps_by_id**](#sort_maps_by_id) - **Output** - - Alignments file, filtered (`.sam`); used in + - Alignments file (`.sam`); used in [**filter_by_indels**](#filter_by_indels) -- **Examples** - -```console -Example 1 | Remove duplicates - -IN: - 1-2 0 19 44414 1 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * HI:i:0 NH:i:1 NM:i:0 MD:Z:21 RG:Z:A1 YZ:Z:0 - 1-2 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * NM:i:0 MD:Z:21 NH:i:1 -OUT: - 1-2 0 19 44414 255 21M * 0 0 GAAGGCGCTTCCCTTTGGAGT * MD:Z:21 NH:i:1 NM:i:0 - - -Example 2 | Remove inferiors single alignment - -IN: - 1-704 16 19 207362 1 18M * 0 0 CCCGGGCCCGGCGCGCCG * HI:i:0 NH:i:2 NM:i:0 MD:Z:18 RG:Z:A1 YZ:Z:0 - 1-704 272 19 471264 1 16M1I1M * 0 0 CCCGGGCCCGGCGCGCCG * HI:i:1 NH:i:2 NM:i:2 MD:Z:11G5 RG:Z:A1 YZ:Z:0 -OUT: - 1-704 16 19 207362 1 18M * 0 0 CCCGGGCCCGGCGCGCCG * HI:i:0 NH:i:1 NM:i:0 MD:Z:18 RG:Z:A1 YZ:Z:0 - - -Example 3 | Remove inferiors multiple alignments - -IN: - - 1-1197 0 19 56327 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:0 NH:i:4 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 - 1-1197 256 19 68983 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:1 NH:i:4 NM:i:3 MD:Z:1C10AT1 RG:Z:A1 YZ:Z:0 - 1-1197 256 19 76967 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:2 NH:i:4 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 - 1-1197 256 19 92363 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:4 NH:i:4 NM:i:3 MD:Z:1C11TA RG:Z:A1 YZ:Z:0 - -OUT: - 1-1197 0 19 56327 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:0 NH:i:2 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 - 1-1197 256 19 76967 1 15M * 0 0 TATGGCACTGGTAGA * HI:i:1 NH:i:2 NM:i:2 MD:Z:1C11T1 RG:Z:A1 YZ:Z:0 -``` #### `filter_by_indels` -Filter multimappers favoring mismatches over InDels with a +Remove multimappers favoring mismatches over indels with a [**custom script**][custom-script-filter-mm]. -> Under the assumption that InDels are less frequent than mismatches only -> those alignments (of the same read with the same edit distance) with the -> lowest number of InDels are kept. This approach allows the presence of -> multimappers and/or InDels after the filtering if the alignments contain the -> same proportion of mismatches vs. InDels. - - **Input** - - Alignments file, sorted, filtered (`.sam`); from + - Alignments file, sorted (`.sam`); from [**remove_inferiors**](#remove_inferiors) - **Output** - - Alignments file, sorted, filtered (`.sam`); used in + - Alignments file (`.sam`); used in [**convert_all_alns_sam_to_bam**](#convert_all_alns_sam_to_bam) and [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primr) -- **Examples** - -```console -Example 1 | Different proportion of mismatches vs. InDels - -IN: - 1-1 16 19 77595 255 14M1D8M * 0 0 GCAGGAGAATCACTGATGTCAG * MD:Z:14^T2A1C3 NH:i:2 NM:i:3 XA:Z:Q XI:i:1 - 1-1 0 19 330456 255 4M1D1M1I3M1D13M * 0 0 CTGACATCAGTGATTCTCCTGC * MD:Z:4^G4^A13 NH:i:2 NM:i:3 XA:Z:Q XI:i:0 -OUT: - 1-1 16 19 77595 255 14M1D8M * 0 0 GCAGGAGAATCACTGATGTCAG * MD:Z:14^T2A1C3 NM:i:3 XA:Z:Q XI:i:1 NH:i:1 HI:i:1 - - -Example 2 | Equal proportion of mismatches vs. InDels - -IN: - 1-1 0 19 142777 255 15M1I5M * 0 0 GCTAGGTGGGAGGCTTGAAGC * MD:Z:4C0T14 NH:i:3 NM:i:3 XA:Z:Q XI:i:0 - 1-1 16 19 270081 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14G0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:2 - 1-1 16 19 545543 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14A0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:1 -OUT: - 1-1 0 19 142777 255 15M1I5M * 0 0 GCTAGGTGGGAGGCTTGAAGC * MD:Z:4C0T14 NH:i:3 NM:i:3 XA:Z:Q XI:i:0 - 1-1 16 19 270081 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14G0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:2 - 1-1 16 19 545543 255 6M1I14M * 0 0 GCTTCAAGCCTCCCACCTAGC * MD:Z:14A0G4 NH:i:3 NM:i:3 XA:Z:Q XI:i:1 -``` #### `convert_all_alns_sam_to_bam` @@ -1044,10 +814,10 @@ Convert alignments `.sam` file to `.bam` with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -> with pri-miR annotations. +with pri-miR annotations. - **Input** - - Alignments file, filtered (`.sam`); from [**filter_by_indels**](#filter_by_indels) + - Alignments file (`.sam`); from [**filter_by_indels**](#filter_by_indels) - **Output** - Alignments file (`.bam`); used in [**sort_all_alns_bam_by_position**](#sort_all_alns_bam_by_position) @@ -1058,7 +828,7 @@ Convert alignments `.sam` file to `.bam` with Sort alignments by position with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -> with pri-miR annotations more efficiently. +with pri-miR annotations more efficiently. - **Input** - Alignments file (`.bam`); from @@ -1071,16 +841,16 @@ Sort alignments by position with [**SAMtools**](#third-party-software-used). #### `index_all_alns_bam` -Create index BAM file with [**SAMtools**](#third-party-software-used). +Create index `BAM` file with [**SAMtools**](#third-party-software-used). > Indexing is required by genome viewers such as IGV to quickly display -> alignments in a genomic region of interest. +alignments in a genomic region of interest. - **Input** - - Alignments file, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_all_alns_bam_by_position**](#sort_all_alns_bam_by_position) - **Output** - - BAM index file (`.bam.bai`); used in + - `BAM` index file (`.bam.bai`); used in [**intersect_extended_primir**](#intersect_extended_primir) @@ -1095,25 +865,24 @@ Target rule as required by [Snakemake][docs-snakemake]. - **Input** - Alignments file, filtered (`.sam`); from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - and [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) + - Alignments file, filtered (`.sam`); from + [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) + - Alignments file, sorted, tagged (`.sam`); from + [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - (iso)miR and/or pri-miR counts table (`.tab`); from [**merge_tables**](#merge_tables) - - Alignments file, uncollapsed, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - BAM index file (`.bam.bai`); from + - `BAM` index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - #### `intersect_extendend_primir` Intersect the aligned reads with the extended pri-miR annotations with [**BEDTools**](#third-party-software-used). -> Only those alignments fully intersecting a (possibly extended) pri-miR -> annotated region are kept. - - **Input** - - Alignments file, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_all_alns_bam_by_position**](#sort_all_alns_bam_by_position) - pri-miR extended annotations (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) @@ -1128,16 +897,14 @@ Intersect the aligned reads with the extended pri-miR annotations with Remove alignments that do not intersect with any pri-miR with [**SAMtools**](#third-party-software-used). -> Required to only intersect alignments within a (possibly extended) pri-miR -> locus. +> Required to only intersect alignments within a pri-miR locus. - **Input** - - Alignments file, filtered (`.sam`); from - [**filter_by_indels**](#filter_by_indels) + - Alignments file (`.sam`); from [**filter_by_indels**](#filter_by_indels) - pri-miR intersections file (`.bed`); from [**intersect_extended_primir**](#intersect_extended_primir) - **Output** - - (**Workflow output**) Alignments file, filtered (`.sam`); used in + - Alignments file, filtered (`.sam`); used in [**convert_intersecting_primir_sam_to_bam**](#convert_intersecting_primir_sam_to_bam) and [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) @@ -1148,10 +915,10 @@ Convert alignments `.sam` file to `.bam` with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -> with miRNA annotations. +with miRNA annotations. - **Input** - - Alignments file, filtered (`.sam`); from + - Alignments file (`.sam`); from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - **Output** - Alignments file (`.bam`); used in @@ -1163,7 +930,7 @@ Convert alignments `.sam` file to `.bam` with Sort alignments by position with [**SAMtools**](#third-party-software-used). > Required by [BEDTools](#third-party-software-used) to intersect alignments -> with miRNA annotations more efficiently. +with miRNA annotations more efficiently. - **Input** - Alignments file (`.bam`); from @@ -1176,16 +943,16 @@ Sort alignments by position with [**SAMtools**](#third-party-software-used). #### `index_intersecting_primir_bam` -Create index BAM file with [**SAMtools**](#third-party-software-used). +Create index `BAM` file with [**SAMtools**](#third-party-software-used). > Indexing is required by genome viewers such as IGV to quickly display -> alignments in a genomic region of interest. +alignments in a genomic region of interest. - **Input** - - Alignments file, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_intersecting_primir_bam_by_position**](#sort_intersecting_primir_bam_by_position) - **Output** - - BAM index file (`.bam.bai`); used in + - `BAM` index file (`.bam.bai`); used in [**intersect_extended_mirna**](#intersect_extended_mirna) @@ -1194,16 +961,13 @@ Create index BAM file with [**SAMtools**](#third-party-software-used). Intersect the aligned reads with the extended miRNA annotations with [**BEDTools**](#third-party-software-used). -> Only those alignments fully intersecting an extended mature miRNA annotated -> region are kept. - - **Input** - - Alignments file, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_intersecting_primir_bam_by_position**](#sort_intersecting_primir_bam_by_position) - - Mature miRNA extended annotations (`.gff3`); from + - miRNA extended annotations (`.gff3`); from [**extend_mirs_annotations**](#extend_mirs_annotations) - **Output** - - Mature miRNA intersections file (`.bed`); used in + - miRNA intersections file (`.bed`); used in [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) and [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) @@ -1216,12 +980,12 @@ Remove alignments that do not intersect with any miRNA with > Required to efficiently classify the alignments. - **Input** - - Alignments file, filtered (`.sam`); from + - Alignments file (`.sam`); from [**filter_sam_by_intersecting_primir**](#filter_sam_by_intersecting_primir) - - Mature miRNA intersections file (`.bed`); from + - miRNA intersections file (`.bed`); from [**intersect_extended_mirna**](#intersect_extended_mirna) - **Output** - - (**Workflow output**) Alignments file, filtered (`.sam`); used in + - Alignments file, filtered (`.sam`); used in [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) and [**uncollapse_reads**](#uncollapse_reads) @@ -1231,72 +995,29 @@ Remove alignments that do not intersect with any miRNA with Classify and add the intersecting (iso)miR to each alignment as a tag with a [**custom script**][custom-script-iso-tag]. -> In this step, the mature miRNA annotated regions are used instead of the -> extended ones. Each alignment gets an extra tag (`YW:Z`) with either the -> (iso)miR(s) it is considered to really intersect with or an empty string -> otherwise. The format of the intersecting mature miRNA species is -> `miRNA_name|5p-shift|3p-shift|CIGAR|MD|read_name`, where `5p-shift` and -> `3p-shift` are the difference between the miRNA start and end coordinates and -> the alignment's ones respectively. +> To classify the reads, miRNA annotations are turned into the original ones. +The alignment start and end shifts relative to the annotations are computed +and append along with the `CIGAR` and `MD` strings to the intersecting miRNA. +If the read is classified as a canonical miRNA, the name will not include +the star and end shift, nor the `CIGAR` and `MD` strings. - **Input** - - Alignments file, filtered (`.sam`); from + - Alignments file (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - - Mature miRNA intersections file (`.bed`); from + - miRNA intersections file (`.bed`); from [**intersect_extended_mirna**](#intersect_extended_mirna) - **Parameters** - **config_template.yaml** - `extension`: Number of nucleotides by which mature miRNA annotated - regions are extended (default: 6) + regions are extended (default 6) - **Output** - Alignments file, tagged (`.sam`); used in [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) -- **Examples** - -```console -Example 1 | Intersecting a canoncial mature miRNA - -IN miRNA annotations: - chr19 . miRNA 44377 44398 . + . ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160 -IN SAM record: - 1-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 -NEW TAG: - YW:Z:hsa-miR-524-5p|0|0|22M|22|CTACAAAGGGAAGCACTTTCTC - - -Example 2 | Intersecting an isomiR (no shifts) - -IN miRNA annotations: - chr19 . miRNA 44377 44398 . + . ID=MIMAT0002849;Alias=MIMAT0002849;Name=hsa-miR-524-5p;Derives_from=MI0003160 -IN SAM record: - 1-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 -NEW TAG: - YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22|CTACAAAGGGAGGTAGCACTTTCTC - -Example 3 | Intersecting an isomiR (no InDels nor mismatches) - -IN miRNA annotations: - chr19 . miRNA 5338 5359 . + . ID=MIMAT0005795;Alias=MIMAT0005795;Name=hsa-miR-1323;Derives_from=MI0003786 -IN SAM record: - 1-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 -NEW TAG: - YW:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC - - -Example 4 | Not intersecting an (iso)miR - -IN miRNA annotations: - chr19 . miRNA 5338 5359 . + . ID=MIMAT0005795;Alias=MIMAT0005795;Name=hsa-miR-1323;Derives_from=MI0003786 -IN SAM record: - 1-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 -NEW TAG: - YW:Z: -``` #### `sort_intersecting_mirna_by_feat_tag` -Sort the alignments by the tag containing the classified intersecting (iso)miR +Sort the alignments by the tag containing the classified intersecting miRNA with [**SAMtools**](#third-party-software-used). > Required for an efficient quantification. @@ -1311,102 +1032,24 @@ with [**SAMtools**](#third-party-software-used). #### `quantify_mirna` -Tabulate alignments according to its new tag (`YW:Z`) with a +Tabulate alignments according to its tag with a [**custom script**][custom-script-mir-quant]. -> Each alignment contributes to the miRNA species in its `YW:Z` tag by `R/N`, -> where `R` is the number of collapsed reads in that alignment, and `N` is the -> number of genomic and/or transcriptomic loci it aligns to. The values of -> both, `R` and `N` are inferred from the sequence name which follows the -> format `ID-R_N`. The resulting table has a row for each mature miRNA species -> (isomiR, canonical miRNA or both) with the name format set in -> [**add_intersecting_mirna_tag**](#add_intersecting_mirna_tag) unless -> considered a canonical miRNA, which only keeps the annotated mature miRNA -> name. A miRNA species is considered to be canonical if there are no shifts -> between its start and end positions and the aligned read ones, and there -> are no mismatches nor InDels. - -- **Input** - - Alignments file, tagged, sorted (`.sam`); from +> Quantification is done with partial counts (_i.e._ each alignment contributes +by the number of collapsed reads divided by the number of hits). + +- **Input** + - Alignments file, sorted, tagged (`.sam`); from [**sort_intersecting_mirna_by_feat_tag**](#sort_intersecting_mirna_by_feat_tag) - **Parameters** - **samples.tsv** - - Library name; specified in the sample's table column `sample` + - Library name; specify in sample table column `sample` - **config_template.yaml** - - `mir_list`: miRNA features to be quantified (default: isomir, mirna + - `mir_list`: miRNA features to be quantified (default isomir, mirna pri-miR) - **Output** - (iso)miR counts tab-delimited file; used in [**merge_tables**](#merge_tables) -- **Examples** - -```console -Example 1 | Canonical miRNA and isomiR - -IN SAM record: - 10-4_2 0 19 34627 255 21M * 0 0 AAAGTGCTTCCTTTTAGAGGG * MD:Z:21 NM:i:0 NH:i:2 HI:i:1 YW:Z:hsa-miR-520b-3p|0|0|21M|21 - 10-4_2 0 19 40866 255 21M * 0 0 AAAGTGCTTCCTTTTAGAGGG * MD:Z:21 NM:i:0 NH:i:2 HI:i:2 YW:Z:hsa-miR-520c-3p|0|-1|21M|21 - -Data: - Alignment: - Read ID: 10 - Number of collapsed reads: 4 - Number of mapped genomic loci: 2 - Contribution: 4/2 = 2 - - miRNA species: - Tag name: hsa-miR-520b-3p|0|0|21M|21|AAAGTGCTTCCTTTTAGAGGG - Type: Canonical - Table name: hsa-miR-520b-3p - Total count: 2 - - Tag name: hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG - Type: isomiR - Table name: hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG - Total count: 2 - -OUT table: - ID lib_name - hsa-miR-520b-3p 2 - hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG 2 - - -Example 2 | Different isomiRs - -IN SAM record: - 599-1_3 0 19 27804 255 20M * 0 0 AAAGTGCTTCCTTTTAGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:1 YW:Z:hsa-miR-526b-3p|1|-1|20M|20 - 599-1_3 0 19 34627 255 20M * 0 0 AAAGTGCTTCCTTTTAGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:2 YW:Z:hsa-miR-520b-3p|0|-1|20M|20 - 599-1_3 0 19 40866 255 20M * 0 0 AAAGTGCTTCCTTTTAGAGG * MD:Z:20 NM:i:0 NH:i:3 HI:i:3 YW:Z:hsa-miR-520c-3p|0|-2|20M|20 - -Data: - Alignment: - Read ID: 599 - Number of collapsed reads: 1 - Number of mapped genomic loci: 3 - Contribution: 1/3 = 0.33 - - miRNA species: - Tag name: hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG - Type: isomiR - Table name: hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG - Total count: 0.33 - - Tag name: hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG - Type: isomiR - Table name: hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG - Total count: 0.33 - - Tag name: hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG - Type: isomiR - Table name: hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG - Total count: 0.33 - -OUT table: - ID lib_name - hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 - hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 - hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 -``` #### `quantify_primir` @@ -1414,73 +1057,15 @@ OUT table: Tabulate alignments according to its intersecting pri-miR with a [**custom script**][custom-script-pri-quant] -> Each alignment contributes to the pri-miR it intersects with by `R/N`, where -> `R` is the number of collapsed reads in that alignment, and `N` is the -> number of genomic and/or transcriptomic loci it aligns to. The values of -> both, `R` and `N` are inferred from the sequence name which follows the -> format `ID-R_N`. The resulting table has a row for each pri-miR with the -> name format set in [**mirna_extension**](#mirna_extension). +> Quantification is done with partial counts (_i.e._ each alignment contributes +by the number of collapsed reads divided by the number of hits). - **Input** - pri-miR intersections file (`.bed`); from - [**intersect_extended_primir**](#intersect_extended_primir) + [**intersecti_extended_primir**](#intersect_extended_primir) - **Output** - pri-miR counts tab-delimited file; used in [**merge_tables**](#merge_tables) -- **Examples** - -```console -Example 1 | One single pri-miR with different alignments - -IN BED records: - 19 . miRNA_primary_transcript 27766 27788 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27765 27788 68-2_1 255 + - 19 . miRNA_primary_transcript 27766 27787 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27765 27787 316-1_7 1 + - 19 . miRNA_primary_transcript 27804 27823 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27803 27823 599-1_3 255 + - 19 . miRNA_primary_transcript 27805 27822 . + . ID=MI0003150;Alias=MI0003150;Name=hsa-mir-526b_-0_+0 19 27804 27822 226-1_4 1 + - -Alignments: - Read ID: 68 - Number of collapsed reads: 2 - Number of mapped genomic loci: 1 - Contribution: 2/1 = 2 - - Read ID: 316 - Number of collapsed reads: 1 - Number of mapped genomic loci: 7 - Contribution: 1/7 = 0.143 - - Read ID: 599 - Number of collapsed reads: 1 - Number of mapped genomic loci: 3 - Contribution: 1/3 = 0.33 - - Read ID: 226 - Number of collapsed reads: 1 - Number of mapped genomic loci: 4 - Contribution: 1/4 = 0.25 - -OUT table: - ID lib_name - hsa-mir-526b_-0_+0 2.723 - - -Example 2 | Different pri-miRs for a single read - -IN BED records: - 19 . miRNA_primary_transcript 40866 40886 . + . ID=MI0003158;Alias=MI0003158;Name=hsa-mir-520c_-0_+0 19 40865 40886 10-4_2 255 + - 19 . miRNA_primary_transcript 34627 34647 . + . ID=MI0003155;Alias=MI0003155;Name=hsa-mir-520b_-5_+6 19 34626 34647 10-4_2 255 + - -Alignment: - Read ID: 10 - Number of collapsed reads: 4 - Number of mapped genomic loci: 2 - Contribution: 4/2 = 2 - -OUT table: - ID lib_name - hsa-mir-520c_-0_+0 2 - hsa-mir-520b_-5_+6 2 -``` #### `merge_tables` @@ -1488,56 +1073,24 @@ OUT table: Merge all the tables from the different libraries into a single one with a [**custom script**][custom-script-merge-tab]. -> The final table(s) containing the counting data from all libraries for the -> (iso)miRs and/or pri-miRs have a row per miRNA species and a column per -> sample library. If a miRNA species is not found in a certain library, its -> value is set to `NA`. - - **Input** - - Counts tab-delimited file; from [**quantify_mirna**](#quantify_mirna) + - counts tab-delimited file; from [**quantify_mirna**](#quantify_mirna) and/or [**quantify_primir**](#quantify_primir) - **Parameters** - **cluster_schema.json** - - `mir_list`: miRNA features to be quantified (default: isomir, mirna + - `mir_list`: miRNA features to be quantified (default isomir, mirna pri-mir) - **Output** - - (**Workflow output**) (iso)miR and/or pri-miR counts table (`.tab`) -- **Example** - -```console -IN library 1 - ID lib_1 - hsa-miR-524-5p 1 - hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 1 - hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC 1 - -IN library 2 - ID lib_2 - hsa-miR-524-5p 1 - hsa-miR-1283 1 - hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC 1 - -IN library 3 - ID lib_3 - -OUT table - ID lib_1 lib_2 lib_3 - hsa-miR-524-5p 1 1 NA - hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 1 NA NA - hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC 1 NA NA - hsa-miR-1283 NA 1 NA - hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC NA 1 NA -``` + - (iso)miR and/or pri-miR counts table (`.tab`) #### `uncollapse_reads` Reverse the collapsing of reads with identical sequences as done with -[**FASTX-Toolkit**](#third-party-software-used) with a -[**custom script**][custom-script-uncollapse]. +[**FASTX-Toolkit**](#third-party-software-used). - **Input** - - Alignments file, filtered (`.sam`); from + - Alignments file (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - **Output** - Uncollapsed aligned reads (`.sam`); used in @@ -1550,10 +1103,10 @@ Convert alignments `.sam` file to `.bam` with [**SAMtools**](#third-party-software-used). - **Input** - - Alignments file, uncollapsed (`.sam`); from + - Alignments file (`.sam`); from [**filter_sam_by_intersecting_mirna**](#filter_sam_by_intersecting_mirna) - **Output** - - Alignments file, uncollapsed (`.bam`); used in + - Alignments file (`.bam`); used in [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) @@ -1562,10 +1115,11 @@ Convert alignments `.sam` file to `.bam` with Sort alignments by position with [**SAMtools**](#third-party-software-used). - **Input** - - Alignments file, uncollapsed (`.bam`); from + - Alignments file (`.bam`); from [**convert_uncollapsed_reads_sam_to_bam**](#convert_uncollapsed_reads_sam_to_bam) - **Output** - - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); used in + - Alignments file, sorted (`.bam`); used in + [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam), [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -1573,16 +1127,16 @@ Sort alignments by position with [**SAMtools**](#third-party-software-used). #### `index_uncollapsed_reads_bam` -Create index BAM file with [**SAMtools**](#third-party-software-used). +Create index `BAM` file with [**SAMtools**](#third-party-software-used). > Indexing is required by genome viewers such as IGV to quickly display -> alignments in a genomic region of interest. +alignments in a genomic region of interest. - **Input** - - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - **Output** - - (**Workflow output**) BAM index file (`.bam.bai`); used in + - `BAM` index file (`.bam.bai`); used in [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -1597,7 +1151,7 @@ Target rule as required by [Snakemake][docs-snakemake]. > Local rule - **Input** - - (**Workflow output**) Empty text file (`.txt`) + - Empty text files (`.txt`); from [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups) and [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) @@ -1615,7 +1169,7 @@ Create an empty BED file if the user has not provided one. - `bed_file`: BED6 file with all the desired annotation regions to perform the ASCII-style alignment pileups on. (Default: None) - **Output** - - Empty BED file (`.bed`); used in + - BED empty file (`.bed`); used in [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -1623,16 +1177,17 @@ Create an empty BED file if the user has not provided one. #### `compress_reference_genome` -Compress the processed genome with trimmed IDs using `bgzip` with -[**SAMtools**](#third-party-software-used). +Compress the processed genome with trimmed IDs using `bgzip`. > Required to perform the ASCII-style alignment pileups. +> In order to be able to use the `bgzip` command when running the workflow +> using Singularity, [**SAMtools**](#third-party-software-used) is used. - **Input** - - Genome sequence, trimmed IDs (`.fa`); from + - Genome sequence file, trimmed IDs (`.fa`); from [**trim_genome_seq_ids**](#trim_genome_seq_ids) - **Output** - - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); used in + - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); used in [**create_per_library_ascii_pileups**](#create_per_library_ascii_pileups), [**create_per_run_ascii_pileups**](#create_per_run_ascii_pileups) and/or [**create_per_condition_ascii_pileups**](#create_per_condition_ascii_pileups) @@ -1641,55 +1196,55 @@ Compress the processed genome with trimmed IDs using `bgzip` with #### `create_per_library_ascii_pileups` Create ASCII-style pileups for all the desired annotated regions across -libraries with [**ASCII-style alignment pileups**](#third-party-software-used). +libraries with [**ASCII-style alignment pilueups**](#third-party-software-used). > A directory containing the ASCII-style pileups is created for each > library. If no BED file is provided, the pileups' output directories will > only contain an empty file. - **Input** - - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); from + - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); from [**compress_reference_genome**](#compress_reference_genome) - - miRNA annotations, mapped chromosome name(s) (`.gff3`); from + - miRNA annotations with mapped genes(`.gff3`); from [**map_chr_names**](#map_chr_names) - - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - (**Workflow output**) BAM index file (`.bam.bai`); used in + - `BAM` index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - Annotated genomic regions (`.bed`); from workflow input files or [**create_empty_bed**](#create_empty_bed) - **Output** - - (**Workflow output**) Empty text file (`.txt`) + - Empty text file (`.txt`) #### `create_per_run_ascii_pileups` Create ASCII-style pileups for all the desired annotated regions for the whole -run with [**ASCII-style alignment pileups**](#third-party-software-used). +run with [**ASCII-style alignment pilueups**](#third-party-software-used). > If no BED file is provided, the pileups' output directory will only contain > an empty file. - **Input** - - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); from + - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); from [**compress_reference_genome**](#compress_reference_genome) - - miRNA annotations, mapped chromosome name(s) (`.gff3`); from + - miRNA annotations with mapped genes(`.gff3`); from [**map_chr_names**](#map_chr_names) - - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - (**Workflow output**) BAM index file (`.bam.bai`); used in + - `BAM` index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - Annotated genomic regions (`.bed`); from workflow input files or [**create_empty_bed**](#create_empty_bed) - **Output** - - (**Workflow output**) Empty text file (`.txt`) + - Empty text file (`.txt`) #### `create_per_condition_ascii_pileups` Create ASCII-style pileups for all the desired annotated regions across the different library subsets if provided with -[**ASCII-style alignment pileups**](#third-party-software-used). +[**ASCII-style alignment pilueups**](#third-party-software-used). > **OPTIONAL RULE.** The ASCII-style pileups for each annotated region are > made if, and only if, at least one library subset is specified in the @@ -1697,21 +1252,21 @@ different library subsets if provided with > executed, and no output will be generated. - **Input** - - Genome sequence, trimmed IDs, `bgzip`ed (`.fa.bz`); from + - Genome sequence file, trimmed IDs, `bgzip`ed (`.fa.bz`); from [**compress_reference_genome**](#compress_reference_genome) - - miRNA annotations, mapped chromosome name(s) (`.gff3`); from + - miRNA annotations with mapped genes(`.gff3`); from [**map_chr_names**](#map_chr_names) - - (**Workflow output**) Alignments file, uncollapsed, sorted (`.bam`); from + - Alignments file (`.bam`); from [**sort_uncollapsed_reads_bam_by_position**](#sort_uncollapsed_reads_bam_by_position) - - (**Workflow output**) BAM index file (`.bam.bai`); used in + - `BAM` index file (`.bam.bai`); from [**index_uncollapsed_reads_bam**](#index_uncollapsed_reads_bam) - Annotated genomic regions (`.bed`); from workflow input files or [**create_empty_bed**](#create_empty_bed) - **Parameters** - **config_template.yaml** - - `lib_dict`: Dictionary of arbitrary condition names (keys) and library - names to aggregate alignment pileups for (values; MUST correspond to names - in samples table) (default: None) + - `lib_dict`: Subset(s) of library name(s), as specified in the samples' + table column `sample` and the subset identifier stored in a dictionary. + (default: None) - **Output** - Empty text file (`.txt`) @@ -1757,7 +1312,6 @@ different library subsets if provided with [license-gpl2]: [license-gpl3]: [license-mit]: -[oligomap-out]: [pub-bedtools]: [pub-cufflinks]: [pub-cutadapt]: From 032af379bd8355e658a3ecf644a7356a8e3c3af4 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:33:28 +0200 Subject: [PATCH 30/42] ci: fix static code analysis --- scripts/mirna_quantification.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/scripts/mirna_quantification.py b/scripts/mirna_quantification.py index ef29e8c..0d0def4 100755 --- a/scripts/mirna_quantification.py +++ b/scripts/mirna_quantification.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +# pylint: disable=line-too-long + """Quantify miRNAs and corresponding isomiRs. Read the input SAM file, calculate the contribution sum of the intersecting @@ -115,7 +117,8 @@ command: mirna_quantification.py SAM --count --len --mir-list isomir output: hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTAA 4.333333333333333 6 23 hsa-miR-512-3p|0|1|23M|3T18C0|AAGGGCTGTCATAGCTGAGGTAA 12.0 8 19 -""" +""" # noqa: E501 +# pylint: enable=line-too-long import argparse from pathlib import Path @@ -285,7 +288,6 @@ def collapsed_contribution(aln: pysam.AlignedSegment) -> float: Alignment to which the overall contribution is calculated Returns: - Contribution of alignment to overall count """ name = str(aln.query_name) @@ -372,7 +374,8 @@ def get_name(pre_name: str) -> list[str]: Args: pre_name: - string with the format FEAT_NAME|5p-SHIFT|3p-SHIFT|CIGAR|MD|READ_SEQ + string with the format + FEAT_NAME|5p-SHIFT|3p-SHIFT|CIGAR|MD|READ_SEQ Returns: list with the species name to be found in the final table and its type From 55712c7b4d5d76957975d1aee91067d9929e5ff9 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:37:18 +0200 Subject: [PATCH 31/42] ci: fix static code analysis --- scripts/iso_name_tagging.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index 035cb1b..caa5f55 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -157,7 +157,7 @@ def attributes_dictionary(attr: str) -> Dict[str, str]: def parse_intersect_output( - intersect_file: Path, id: str = "name", extension: int = 0 + intersect_file: Path, ID: str = "name", extension: int = 0 ) -> Optional[Dict[Optional[str], list]]: """Parse intersect BED file. @@ -205,7 +205,7 @@ def parse_intersect_output( for line in bedfile: fields = Fields(*line.strip().split("\t")) - miRNA_name = attributes_dictionary(fields.feat_attributes)[id] + miRNA_name = attributes_dictionary(fields.feat_attributes)[ID] miRNA_start = int(fields.feat_start) + extension miRNA_end = int(fields.feat_end) - extension @@ -268,7 +268,7 @@ def main(args) -> None: """Add intersecting feature(s) into a SAM file as a tag.""" intersect_data = parse_intersect_output( intersect_file=args.bed, - id=args.id, + ID=args.id, extension=args.extension, ) From ce0d897c45741118b775ca7c04d9b45bd7ea09e5 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:38:24 +0200 Subject: [PATCH 32/42] ci: fix static code analysis --- scripts/tests/test_iso_name_tagging.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/tests/test_iso_name_tagging.py b/scripts/tests/test_iso_name_tagging.py index fe4c1a6..6429e17 100644 --- a/scripts/tests/test_iso_name_tagging.py +++ b/scripts/tests/test_iso_name_tagging.py @@ -243,7 +243,7 @@ def test_parse_intersect_output_alias_id(self, bed_sam, intersect_dicts): in_bed, in_sam, out_f = bed_sam out_name, out_id_alias, out_ext_3 = intersect_dicts - out_inter = parse_intersect_output(intersect_file=in_bed, id="alias") + out_inter = parse_intersect_output(intersect_file=in_bed, ID="alias") assert sorted(out_inter.items()) == sorted(out_id_alias.items()) @@ -252,7 +252,7 @@ def test_parse_intersect_output_id_id(self, bed_sam, intersect_dicts): in_bed, in_sam, out_f = bed_sam out_name, out_id_alias, out_ext_3 = intersect_dicts - out_inter = parse_intersect_output(intersect_file=in_bed, id="id") + out_inter = parse_intersect_output(intersect_file=in_bed, ID="id") assert sorted(out_inter.items()) == sorted(out_id_alias.items()) From fcc5ac45c4ca314506e6e74f37ec6bec363888f5 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 18 Aug 2024 19:41:00 +0200 Subject: [PATCH 33/42] ci: fix static code analysis --- scripts/iso_name_tagging.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index caa5f55..64a8a3a 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -267,9 +267,9 @@ def get_tags( def main(args) -> None: """Add intersecting feature(s) into a SAM file as a tag.""" intersect_data = parse_intersect_output( - intersect_file=args.bed, - ID=args.id, - extension=args.extension, + intersect_file=args.bed, + ID=args.id, + extension=args.extension, ) with pysam.AlignmentFile(args.sam, "r") as samfile: From 012645d8ab5b1920d42a820b326021a3be9daf28 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Mon, 19 Aug 2024 12:31:36 +0200 Subject: [PATCH 34/42] docs: add new isomiR notation --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 68a49f6..4c6c24d 100644 --- a/README.md +++ b/README.md @@ -420,7 +420,7 @@ InDel or a mismatch on its sequence when compared to the canonical miRNA it maps and intersects with. _MIRFLOWZ_ employs an unambiguous notation to classify isomiRs using the -format `miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and +format `miRNA_name|5p-shift|3p-shift|CIGAR|MD|read_seq`, where `5p-shift` and `3p-shift` represent the differences between the annotated mature miRNA start and end positions and those of the read alignment, respectively. From a516667f32f1c8321a622f179af8d90824672349 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Mon, 19 Aug 2024 12:31:45 +0200 Subject: [PATCH 35/42] docs: add new isomiR notation --- pipeline_documentation.md | 74 +++++++++++++++++++-------------------- 1 file changed, 37 insertions(+), 37 deletions(-) diff --git a/pipeline_documentation.md b/pipeline_documentation.md index 7e1c6c2..6332027 100644 --- a/pipeline_documentation.md +++ b/pipeline_documentation.md @@ -1235,9 +1235,9 @@ with a [**custom script**][custom-script-iso-tag]. > extended ones. Each alignment gets an extra tag (`YW:Z`) with either the > (iso)miR(s) it is considered to really intersect with or an empty string > otherwise. The format of the intersecting mature miRNA species is -> `miRNA_name|5p-shift|3p-shift|CIGAR|MD`, where `5p-shift` and `3p-shift` are -> the difference between the miRNA start and end coordinates and the -> alignment's ones respectively. +> `miRNA_name|5p-shift|3p-shift|CIGAR|MD|read_name`, where `5p-shift` and +> `3p-shift` are the difference between the miRNA start and end coordinates and +> the alignment's ones respectively. - **Input** - Alignments file, filtered (`.sam`); from @@ -1261,7 +1261,7 @@ IN miRNA annotations: IN SAM record: 1-1_1 0 19 44377 255 22M * 0 0 CTACAAAGGGAAGCACTTTCTC * MD:Z:22 NH:i:1 NM:i:0 NEW TAG: - YW:Z:hsa-miR-524-5p|0|0|22M|22 + YW:Z:hsa-miR-524-5p|0|0|22M|22|CTACAAAGGGAAGCACTTTCTC Example 2 | Intersecting an isomiR (no shifts) @@ -1271,7 +1271,7 @@ IN miRNA annotations: IN SAM record: 1-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 NEW TAG: - YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22 + YW:Z:hsa-miR-524-5p|0|0|11M3I11M|22|CTACAAAGGGAGGTAGCACTTTCTC Example 3 | Intersecting an isomiR (no InDels nor mismatches) @@ -1281,7 +1281,7 @@ IN miRNA annotations: IN SAM record: 1-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 NEW TAG: - YW:Z:hsa-miR-1323|0|-1|21M|21 + YW:Z:hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC Example 4 | Not intersecting an (iso)miR @@ -1355,20 +1355,20 @@ Data: Contribution: 4/2 = 2 miRNA species: - Tag name: hsa-miR-520b-3p|0|0|21M|21 + Tag name: hsa-miR-520b-3p|0|0|21M|21|AAAGTGCTTCCTTTTAGAGGG Type: Canonical Table name: hsa-miR-520b-3p Total count: 2 - Tag name: hsa-miR-520c-3p|0|-1|21M|21 + Tag name: hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG Type: isomiR - Table name: hsa-miR-520c-3p|0|-1|21M|21 + Table name: hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG Total count: 2 OUT table: - ID lib_name - hsa-miR-520b-3p 2 - hsa-miR-520c-3p|0|-1|21M|21 2 + ID lib_name + hsa-miR-520b-3p 2 + hsa-miR-520c-3p|0|-1|21M|21|AAAGTGCTTCCTTTTAGAGGG 2 Example 2 | Different isomiRs @@ -1386,26 +1386,26 @@ Data: Contribution: 1/3 = 0.33 miRNA species: - Tag name: hsa-miR-526b-3p|1|-1|20M|20 + Tag name: hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Type: isomiR - Table name: hsa-miR-526b-3p|1|-1|20M|20 + Table name: hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Total count: 0.33 - Tag name: hsa-miR-520b-3p|0|-1|20M|20 + Tag name: hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Type: isomiR - Table name: hsa-miR-520b-3p|0|-1|20M|20 + Table name: hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG Total count: 0.33 - Tag name: hsa-miR-520c-3p|0|-2|20M|20 + Tag name: hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG Type: isomiR - Table name: hsa-miR-520c-3p|0|-2|20M|20 + Table name: hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG Total count: 0.33 OUT table: - ID lib_name - hsa-miR-520b-3p|0|-1|20M|20 0.33 - hsa-miR-520c-3p|0|-2|20M|20 0.33 - hsa-miR-526b-3p|1|-1|20M|20 0.33 + ID lib_name + hsa-miR-520b-3p|0|-1|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 + hsa-miR-520c-3p|0|-2|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 + hsa-miR-526b-3p|1|-1|20M|20|AAAGTGCTTCCTTTTAGAGG 0.33 ``` @@ -1506,27 +1506,27 @@ Merge all the tables from the different libraries into a single one with a ```console IN library 1 - ID lib_1 - hsa-miR-524-5p 1 - hsa-miR-524-5p|0|0|22M|9G12 1 - hsa-miR-524-5p|0|0|22M|9G9C2 1 + ID lib_1 + hsa-miR-524-5p 1 + hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 1 + hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC 1 IN library 2 - ID lib_2 - hsa-miR-524-5p 1 - hsa-miR-1283 1 - hsa-miR-1283|-1|-2|21M|21 1 + ID lib_2 + hsa-miR-524-5p 1 + hsa-miR-1283 1 + hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC 1 IN library 3 - ID lib_3 + ID lib_3 OUT table - ID lib_1 lib_2 lib_3 - hsa-miR-524-5p 1 1 NA - hsa-miR-524-5p|0|0|22M|9G12 1 NA NA - hsa-miR-524-5p|0|0|22M|9G9C2 1 NA NA - hsa-miR-1283 NA 1 NA - hsa-miR-1283|-1|-2|21M|21 NA 1 NA + ID lib_1 lib_2 lib_3 + hsa-miR-524-5p 1 1 NA + hsa-miR-524-5p|0|0|22M|9G12|CTACAAAGGTAAGCACTTTCTC 1 NA NA + hsa-miR-524-5p|0|0|22M|9G9C2|CTACAAAGGTAAGCACTTTATC 1 NA NA + hsa-miR-1283 NA 1 NA + hsa-miR-498-3p|0|0|23M|8T14|AAAGCACCACCAGAGCTTGAAGC NA 1 NA ``` From ccfd5047e0eea3a59dc2f6602161e5d5ad2e4feb Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sat, 31 Aug 2024 22:56:45 +0200 Subject: [PATCH 36/42] test: remove duplicated file --- .../files/reads_ids_iso_mirna_quantification | 160 ------------------ 1 file changed, 160 deletions(-) delete mode 100644 scripts/tests/files/reads_ids_iso_mirna_quantification diff --git a/scripts/tests/files/reads_ids_iso_mirna_quantification b/scripts/tests/files/reads_ids_iso_mirna_quantification deleted file mode 100644 index 18bab50..0000000 --- a/scripts/tests/files/reads_ids_iso_mirna_quantification +++ /dev/null @@ -1,160 +0,0 @@ -hsa-miR-1323|0|-1|21M|21|TCAAAACTGAGGGGCATTTTC 1.0 709268-1_1 -hsa-miR-1323 1.0 528546-1_1 -hsa-miR-371a-5p 1.0 270342-1_1 -hsa-miR-371a-5p|0|3|23M|17A3T0C0|ACTCAAACTGTGGGGGCACTTAG 1.0 840419-1_1 -hsa-miR-371b-3p|0|-1|22M|22|GCACTCAAACTGTGGGGGCACT 2.0 120522-2_1 -hsa-miR-372-3p|0|-1|22M|0A0A2T17|CGAGCGCTGCGACATTTGAGCG 1.0 299969-1_1 -hsa-miR-372-3p|0|-1|22M|22|AAAGTGCTGCGACATTTGAGCG 4.0 67825-4_1 -hsa-miR-372-3p|0|-1|22M|3G18|AAATTGCTGCGACATTTGAGCG 3.0 90583-3_1 -hsa-miR-372-3p|0|0|23M|1A20T0|AGAGTGCTGCGACATTTGAGCGA 1.0 629861-1_1 -hsa-miR-372-3p|0|0|23M|22T|AAAGTGCTGCGACATTTGAGCGA 2.0 120521-2_1 -hsa-miR-372-3p 1.0 739110-1_1 -hsa-miR-372-3p|0|0|23M|3G19|AAATTGCTGCGACATTTGAGCGT 1.0 270338-1_1 -hsa-miR-372-3p|1|0|21M1I1M|23|AAGTGCTGCGACATTTGAGCGAT 1.0 267649-1_1 -hsa-miR-372-3p|1|0|22M|22|AAGTGCTGCGACATTTGAGCGT 1.0 313132-1_1 -hsa-miR-372-3p|1|0|4M1I18M|2G19|AACTTGCTGCGACATTTGAGCGT 1.0 270337-1_1 -hsa-miR-373-3p 2.0 188149-2_1 -hsa-miR-498-5p 1.0 270393-1_1 -hsa-miR-512-3p|-2|-4|3M1I17M|11C3G4|GAACAGTGCTGTGATAACTGA 1.0 610105-1_2;610105-1_2 -hsa-miR-512-3p|0|-1|21M|20T|AAGTGCTGTCATAGCTGAGGA 0.6666666666666666 645839-1_3;645839-1_3 -hsa-miR-512-3p|0|-1|21M|20T0|AAGTGCTGTCATAGCTGAGGA 0.3333333333333333 645839-1_3 -hsa-miR-512-3p|0|-1|21M|21|AAGTGCTGTCATAGCTGAGGT 4.0 67830-4_3;67830-4_3;67830-4_3 -hsa-miR-512-3p|0|-1|21M|7G13|AAGTGCTTTCATAGCTGAGGT 1.0 535182-1_3;535182-1_3;535182-1_3 -hsa-miR-512-3p|0|-2|20M|12A7|AAGTGCTGTCATCGCTGAGG 1.0 766380-1_3;766380-1_3;766380-1_3 -hsa-miR-512-3p|0|-2|20M|20|AAGTGCTGTCATAGCTGAGG 4.0 67831-4_3;67831-4_3;67831-4_3 -hsa-miR-512-3p|0|0|22M|12A9|AAGTGCTGTCATCGCTGAGGTC 1.0 270395-1_3;270395-1_3;270395-1_3 -hsa-miR-512-3p|0|0|22M|17A4|AAGTGCTGTCATAGCTGCGGTC 1.0 773136-1_3;773136-1_3;773136-1_3 -hsa-miR-512-3p|0|0|22M|21C|AAGTGCTGTCATAGCTGCGGTT 2.0 102065-3_3;102065-3_3 -hsa-miR-512-3p|0|0|22M|21C0|AAGTGCTGTCATAGCTGCGGTT 1.0 102065-3_3 -hsa-miR-512-3p 9.0 37896-9_3;37896-9_3;37896-9_3 -hsa-miR-512-3p|0|1|23M|21C0C0|AAGTGCTGTCATAGCTGAGGTAG 1.0 334943-1_2;334943-1_2 -hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 -hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 270401-1_2 -hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 -hsa-miR-512-3p|0|1|23M|22C|AAGTGCTGTCATAGCTGAGGTCA 0.5 270401-1_2 -hsa-miR-512-3p|0|1|23M|22C0|AAGTGCTGTCATAGCTGAGGTCT 0.3333333333333333 270396-1_3 -hsa-miR-512-3p|0|1|23M|3T18C0|AAGAGCTGTCATAGCTGAGGTCT 1.0 673650-1_2;673650-1_2 -hsa-miR-512-5p|1|-1|21M|21|ACTCAGCCTTGAGGGCACTTT 2.0 150819-2_3;150819-2_3;150819-2_3 -hsa-miR-512-5p|1|-2|20M|20|ACTCAGCCTTGAGGGCACTT 1.0 270402-1_3;270402-1_3;270402-1_3 -hsa-miR-512-5p|1|0|22M|22|ACTCAGCCTTGAGGGCACTTTC 1.0 752875-1_3;752875-1_3;752875-1_3 -hsa-miR-515-3p|0|-1|21M|21|GAGTGCCTTCTTTTGGAGCGT 1.0 369314-1_3;369314-1_3;369314-1_3 -hsa-miR-516a-5p|0|-1|22M|22|TTCTCGAGGAAAGAAGCACTTT 6.0 54840-6_3;54840-6_3;54840-6_3 -hsa-miR-516a-5p|1|-1|21M|21|TCTCGAGGAAAGAAGCACTTT 1.0 423555-1_3;423555-1_3;423555-1_3 -hsa-miR-516b-5p|0|-3|19M|18C|ATCTGGAGGTAAGAAGCAA 0.6666666666666666 270365-1_3;270365-1_3 -hsa-miR-516b-5p|0|-3|19M|18C0|ATCTGGAGGTAAGAAGCAA 0.3333333333333333 270365-1_3 -hsa-miR-516b-5p|0|0|22M|10A11|ATCTGGAGGTCAGAAGCACTTT 1.0 270366-1_3;270366-1_3;270366-1_3 -hsa-miR-516b-5p 3.0 86082-3_3;86082-3_3;86082-3_3 -hsa-miR-517-5p|-1|0|23M|22T|CCCTCTAGATGGAAGCACTGTCA 0.6000000000000001 270359-1_5;270359-1_5;270359-1_5 -hsa-miR-517-5p|-1|0|23M|22T0|CCCTCTAGATGGAAGCACTGTCA 0.4 270359-1_5;270359-1_5 -hsa-miR-517-5p|4|2|6M1D13M|0T5^G13|GAGATGAAGCACTGTCTGT 1.0 752904-1_3;752904-1_3;752904-1_3 -hsa-miR-517-5p|4|2|6M1D13M|6^G9C3|TAGATGAAGCACTGTATGT 3.0 105051-3_3;105051-3_3;105051-3_3 -hsa-miR-517a-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 1.3333333333333333 120530-2_3;120530-2_3 -hsa-miR-517a-3p 2.6666666666666665 67957-4_3;67957-4_3 -hsa-miR-517b-3p|0|-1|21M|21|ATCGTGCATCCCTTTAGAGTG 0.6666666666666666 120530-2_3 -hsa-miR-517b-3p 1.3333333333333333 67957-4_3 -hsa-miR-518b 1.0 447402-1_1 -hsa-miR-518c-5p|1|-1|21M|21|CTCTGGAGGGAAGCACTTTCT 1.0 270377-1_1 -hsa-miR-518c-5p|1|-2|20M|19C|CTCTGGAGGGAAGCACTTTA 1.0 751085-1_1 -hsa-miR-518c-5p|1|0|22M|22|CTCTGGAGGGAAGCACTTTCTG 1.0 270378-1_1 -hsa-miR-518d-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 -hsa-miR-518d-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 -hsa-miR-518d-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 95680-3_9;95680-3_9 -hsa-miR-518d-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 -hsa-miR-518d-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.4444444444444444 139675-2_9;139675-2_9 -hsa-miR-518d-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.2222222222222222 531738-1_9;531738-1_9 -hsa-miR-518d-5p 0.2857142857142857 270381-1_7;270381-1_7 -hsa-miR-518e-3p 1.0 270360-1_1 -hsa-miR-518e-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 -hsa-miR-518e-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 2.1818181818181817 18915-24_11 -hsa-miR-518e-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-518e-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.09090909090909091 630277-1_11 -hsa-miR-518e-5p 0.36363636363636365 67687-4_11 -hsa-miR-518e-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.2727272727272727 84523-3_11 -hsa-miR-518f-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 -hsa-miR-518f-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.3333333333333333 95680-3_9 -hsa-miR-518f-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 -hsa-miR-518f-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.2222222222222222 139675-2_9 -hsa-miR-518f-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.1111111111111111 531738-1_9 -hsa-miR-518f-5p 1.0 347693-1_1 -hsa-miR-519a-3p|0|0|22M|3G18|AAATTGCATCCTTTTAGAGTGT 1.0 270348-1_3;270348-1_3;270348-1_3 -hsa-miR-519a-5p|-1|-1|22M|21T|ACTCTAGAGGGAAGCGCTTTCA 1.0 270357-1_1 -hsa-miR-519a-5p|-1|-1|22M|22|ACTCTAGAGGGAAGCGCTTTCT 5.0 58870-5_1 -hsa-miR-519a-5p|-1|-3|20M|20|ACTCTAGAGGGAAGCGCTTT 1.0 270354-1_1 -hsa-miR-519a-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 -hsa-miR-519a-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-519a-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-519a-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-519a-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 -hsa-miR-519a-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-519a-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-519b-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 -hsa-miR-519b-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-519b-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-519b-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-519b-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 -hsa-miR-519b-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-519b-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-519c-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 -hsa-miR-519c-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-519c-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-519c-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-519c-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 -hsa-miR-519c-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-519c-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-519d-3p|0|-1|21M|21|CAAAGTGCCTCCCTTTAGAGT 1.0 270371-1_1 -hsa-miR-519d-3p|0|-2|20M|20|CAAAGTGCCTCCCTTTAGAG 2.0 153079-2_1 -hsa-miR-520a-3p 4.0 67829-4_1 -hsa-miR-520a-3p|0|0|22M|3G18|AAAGTGCTTCCCTTTGGACTGT 1.0 655140-1_1 -hsa-miR-520a-3p|0|1|23M|22T|AAAGTGCTTCCCTTTGGACTGTA 1.0 485300-1_1 -hsa-miR-520a-5p|0|0|21M|19C0T0|CTCCAGAGGGAAGTACTTTGA 1.0 729311-1_1 -hsa-miR-520a-5p|0|0|21M|20T|CTCCAGAGGGAAGTACTTTCG 1.0 720817-1_1 -hsa-miR-520a-5p 2.0 120535-2_1 -hsa-miR-520a-5p|0|1|19M1D2M|19^C0T1|CTCCAGAGGGAAGTACTTTAG 1.0 228043-1_1 -hsa-miR-520a-5p|0|1|19M1I3M|19C0T1|CTCCAGAGGGAAGTACTTTGAAG 1.0 609803-1_1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C0T1T0|CTCCAGAGGGAAGTACTTTAGA 3.0 101076-3_1 -hsa-miR-520a-5p|0|2|19M1D3M|19^C1G0T0|CTCCAGAGGGAAGTACTTTTAA 2.0 127441-2_1 -hsa-miR-520a-5p|0|2|20M1D2M|20^T1T0|CTCCAGAGGGAAGTACTTTCGA 3.0 103161-3_1 -hsa-miR-520a-5p|0|2|23M|19C0T1T0|CTCCAGAGGGAAGTACTTTAAGA 1.0 478794-1_1 -hsa-miR-520b-3p|-1|-1|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 744127-1_5;744127-1_5 -hsa-miR-520b-3p|0|1|22M|22|AAAGTGCTTCCTTTTAGAGGGT 0.6666666666666666 120532-2_3 -hsa-miR-520c-3p|-1|-2|21M|21|GAAAGTGCTTCCTTTTAGAGG 0.4 744127-1_5;744127-1_5 -hsa-miR-520c-3p 1.3333333333333333 120532-2_3;120532-2_3 -hsa-miR-520c-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 -hsa-miR-520c-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.2222222222222222 120527-2_9 -hsa-miR-520c-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 0.6666666666666666 95680-3_9;95680-3_9 -hsa-miR-520c-5p|0|-1|21M|3T16T0|CTCGAGAGGGAAGCACTTTCA 0.2 270379-1_5 -hsa-miR-520c-5p|0|-2|20M|20|CTCGAGAGGGAAGCACTTTC 0.4444444444444444 139675-2_9;139675-2_9 -hsa-miR-520c-5p|0|-3|19M|19|CTCGAGAGGGAAGCACTTT 0.2222222222222222 531738-1_9;531738-1_9 -hsa-miR-520c-5p 0.2857142857142857 270381-1_7;270381-1_7 -hsa-miR-520e-3p 1.0 361022-1_1 -hsa-miR-520e-5p|3|-3|7M1I9M|2G13|AAAATGGGAAGCAGTTT 1.0 772976-1_1 -hsa-miR-520g-3p|1|-2|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.3333333333333333 270368-1_3 -hsa-miR-520g-3p|1|0|23M|23|CAAAGTGCTTCCCTTTAGAGTGT 1.0 270369-1_1 -hsa-miR-520g-5p|-3|-2|12M1D2M1D2M1I6M|12^A2^A8|CCCTCTAGAGGAGCCTGTTCTGT 1.0 138559-2_2 -hsa-miR-520h|1|0|21M|21|CAAAGTGCTTCCCTTTAGAGT 0.6666666666666666 270368-1_3;270368-1_3 -hsa-miR-522-3p|0|0|22M|1A20|AGAATGGTTCCCTTTAGAGTGT 1.0 270358-1_1 -hsa-miR-522-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 -hsa-miR-522-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-522-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-522-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-522-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 -hsa-miR-522-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-522-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-523-5p|0|-1|21M|19C0T0|CTCTAGAGGGAAGCGCTTTAA 0.16666666666666666 676180-1_6 -hsa-miR-523-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 4.363636363636363 18915-24_11;18915-24_11 -hsa-miR-523-5p|0|-2|20M|19C|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-523-5p|0|-2|20M|19C0|CTCTAGAGGGAAGCGCTTTA 0.09090909090909091 270361-1_11 -hsa-miR-523-5p|0|-3|19M|19|CTCTAGAGGGAAGCGCTTT 0.18181818181818182 630277-1_11;630277-1_11 -hsa-miR-523-5p 0.7272727272727273 67687-4_11;67687-4_11 -hsa-miR-523-5p|0|1|23M|23|CTCTAGAGGGAAGCGCTTTCTGT 0.5454545454545454 84523-3_11;84523-3_11 -hsa-miR-524-5p|0|-1|21M|21|CTCTAGAGGGAAGCGCTTTCT 1.0 270375-1_1 -hsa-miR-524-5p|0|-2|20M|20|CTACAAAGGGAAGCACTTTC 1.0 270376-1_1 -hsa-miR-525-5p|0|-1|20M|20|CTCCAGAGGGATGCACTTTC 5.0 57516-5_1 -hsa-miR-525-5p 3.0 102026-3_1 -hsa-miR-526a-5p|0|-1|21M|20T|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 120527-2_9;120527-2_9 -hsa-miR-526a-5p|0|-1|21M|20T0|CTCTAGAGGGAAGCACTTTCA 0.4444444444444444 120527-2_9;120527-2_9 -hsa-miR-526a-5p|0|-1|21M|21|CTCTAGAGGGAAGCACTTTCT 1.3333333333333333 95680-3_9;95680-3_9;95680-3_9;95680-3_9 -hsa-miR-526a-5p|0|-1|21M|3T16T0|CTCTAGAGGGAAGCACTTTCA 0.4 270379-1_5;270379-1_5 -hsa-miR-526a-5p|0|-2|20M|20|CTCTAGAGGGAAGCACTTTC 0.8888888888888888 139675-2_9;139675-2_9;139675-2_9;139675-2_9 -hsa-miR-526a-5p|0|-3|19M|19|CTCTAGAGGGAAGCACTTT 0.4444444444444444 531738-1_9;531738-1_9;531738-1_9;531738-1_9 -hsa-miR-526a-5p 0.42857142857142855 270381-1_7;270381-1_7;270381-1_7 From 85090daaead9557182f171f8b1acdfa07a504a12 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 12 Jan 2025 18:10:51 +0100 Subject: [PATCH 37/42] refactor: add CLI argument --- workflow/rules/quantify.smk | 1 + 1 file changed, 1 insertion(+) diff --git a/workflow/rules/quantify.smk b/workflow/rules/quantify.smk index e3fe767..a858ddf 100644 --- a/workflow/rules/quantify.smk +++ b/workflow/rules/quantify.smk @@ -304,6 +304,7 @@ rule add_intersecting_mirna_tag: --bed {input.intersect} \ --sam {input.alignments} \ --extension {params.extension} \ + --shift {params.extension} \ > {output.sam} \ ) &> {log}" From c40efce6be9431b5ff0e320ca2f396ca4cb242d9 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 12 Jan 2025 18:11:28 +0100 Subject: [PATCH 38/42] refactor: modify tests --- scripts/tests/test_iso_name_tagging.py | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/scripts/tests/test_iso_name_tagging.py b/scripts/tests/test_iso_name_tagging.py index 6429e17..8d4e28b 100644 --- a/scripts/tests/test_iso_name_tagging.py +++ b/scripts/tests/test_iso_name_tagging.py @@ -87,7 +87,6 @@ def alns(): aln1.set_tag("NH", 2) aln1.set_tag("HI", 1) - # Alignment with 3 insertions aln2 = pysam.AlignedSegment() aln2.cigarstring = "21M" aln2.query_name = "8-2_1" @@ -275,9 +274,9 @@ def test_get_tags_within_shift_range_1_extn(self, alns, intersect_dicts): out_name, out_id_alias, out_ext_3 = intersect_dicts tags = get_tags( - intersecting_mirna=out_name[aln_1.query_name], + intersecting_feat=out_name[aln_1.query_name], alignment=aln_1, - extend=1, + shift=1, ) expected = "hsa-miR-524-3p|1|1|21M|21|GAAGGCGCTTCCCTTTGGAGT" @@ -289,9 +288,9 @@ def test_get_tags_out_shift_range(self, alns, intersect_dicts): out_name, out_id_alias, out_ext_3 = intersect_dicts tags = get_tags( - intersecting_mirna=out_name[aln_1.query_name], + intersecting_feat=out_name[aln_1.query_name], alignment=aln_2, - extend=0, + shift=0, ) assert tags == set() @@ -368,6 +367,8 @@ def test_all_input(self, monkeypatch, bed_sam): "alias", "--extension", "6", + "--shift", + "6", ], ) args = parse_arguments().parse_args() @@ -398,7 +399,7 @@ def test_main_empty_bed_file( main(args) captured = capsys.readouterr() - with open(empty_sam, "r") as out_file: + with open(empty_sam, encoding="utf-8") as out_file: assert captured.out == out_file.read() def test_main_empty_sam_file( @@ -423,7 +424,7 @@ def test_main_empty_sam_file( main(args) captured = capsys.readouterr() - with open(empty_sam, "r") as out_file: + with open(empty_sam, encoding="utf-8") as out_file: assert captured.out == out_file.read() def test_main_bed_sam_file(self, monkeypatch, capsys, bed_sam): @@ -445,13 +446,13 @@ def test_main_bed_sam_file(self, monkeypatch, capsys, bed_sam): main(args) captured = capsys.readouterr() - with open(output, "r") as out_file: + with open(output, encoding="utf-8") as out_file: assert captured.out == out_file.read() def test_main_bed_sam_extension_file( self, monkeypatch, capsys, bed_sam_extension ): - """Test main function with extension equals 6.""" + """Test main function with extension and allowed shit equal to 6.""" in_bed, in_sam, output = bed_sam_extension monkeypatch.setattr( @@ -465,13 +466,15 @@ def test_main_bed_sam_extension_file( str(in_sam), "--extension", "6", + "--shift", + "6", ], ) args = parse_arguments().parse_args() main(args) captured = capsys.readouterr() - with open(output, "r") as out_file: + with open(output, encoding="utf-8") as out_file: assert captured.out == out_file.read() def test_main_bed_sam_file_id(self, monkeypatch, capsys, bed_sam_id): @@ -495,5 +498,5 @@ def test_main_bed_sam_file_id(self, monkeypatch, capsys, bed_sam_id): main(args) captured = capsys.readouterr() - with open(output, "r") as out_file: + with open(output, encoding="utf-8") as out_file: assert captured.out == out_file.read() From 6a384eb5a2ada7300334d89602583af573d37607 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 12 Jan 2025 18:40:34 +0100 Subject: [PATCH 39/42] refactor: generalise script and add CLI --- scripts/iso_name_tagging.py | 132 ++++++++++++++++++++++-------------- 1 file changed, 82 insertions(+), 50 deletions(-) diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index 64a8a3a..84c50f0 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -6,27 +6,25 @@ Build new names for the intersecting features from a BED file and add them as a tag to alignments in a SAM file using the format -miRNA_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ. If either the BED or the SAM -file is empty, only the SAM file header is returned. +FEATURE_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ. EXPECTED INPUT FILES The BED file must be the output of a bedtools intersect call with `-a` being a -GFF3 file and `-b` a BAM file. If the GFF3 used in the bedtools intersect call -has the features start and end coordinates extended, the number of additional -nucleotides must be specified using the CLI option `--extension`. The SAM file -must contain only the reads that have an intersecting feature. +GFF3 file and `-b` a BAM file. The SAM file must only +contain alignments with an intersecting feature. If either the BED or the SAM +file is empty, only the SAM file header is returned. NAME CREATION and TAG ADDITION For each alignment, the name of the intersecting feature follows the -format miRNA_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ. The CLI option `--id` -specifies the feature identifier to be used as miRNA_ID from the attributes +format FEATURE_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ. The CLI option `--id` +specifies the feature identifier to be used as FEATURE_ID from the attributes column in the BED file. The 5' and 3' shift values are the difference between -the feature (extended) start and end coordinates and the alignment ones. If -`--extension` is provided, the feature start and end positions are adjusted by -adding and subtracting respectively the given value. If both, the 5' and -3'-end shifts, are within the range +/- extension (or equal 0 if no value is -provided) the feature name is added to the alignment as the new tag "YW". -Multiple intersecting feature names are separated by a semi-colon. +the alignment and its intersecting feature(s) start and end coordinates +respectively. If `--extension` is provided, features start and end positions +are adjusted by adding and subtracting respectively the given value. If +`--shift` is provided, and both, the 5' and 3'-end shifts, are within the +range +/- `--shift` the feature name is added to the alignment as the new tag +"YW". Multiple intersecting feature names are separated by a semi-colon. EXAMPLES Example 1 @@ -40,6 +38,12 @@ "" out SAM record: 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:22 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z: + explanation: + The aligned read has a length of 22 whereas the feature has a length of + 21. As both have the same starting position, there is a 1bp shift at + the 3' end. Given that no extension nor shift are provided in the + script call, no adjustments to the annotated coordinates are made and + no shifts are allowed. Hence, no tag is added. Example 2 in BED record: @@ -52,6 +56,11 @@ hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC out SAM record: 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC + explanation: + The aligned read and the annotated featrue have the same start and end + positions. Given that no extension are provided in the script call, no + coordinates adjustments are made. And there is no shift on ether end, + the new tag is added. Example 3 in BED record: @@ -59,11 +68,17 @@ in SAM record: 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 command: - iso_name_tagging.py -b BED -s SAM --extension 6 + iso_name_tagging.py -b BED -s SAM --extension 6 --shift 7 new name: hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC out SAM record: 48-1_1 0 19 5338 255 21M * 0 0 TCAAAACTGAGGGGCATTTTC * MD:Z:21 NH:i:1 NM:i:0 YW:Z:hsa-miR-1323|0|0|21M|21|TCAAAACTGAGGGGCATTTTC + explanation: + The feature's start and end coordinates are adjusted by amount of bp + specified by the CLI argument `--extension`. The alignment start and + end positions differ from the adjusted miRNA ones by 6 bp. As there is + a +/- 7 bp shift allowed and both shifts are within this range, the new + tag is added. Example 4 in BED record: @@ -71,11 +86,17 @@ in SAM record: 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:25 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 command: - iso_name_tagging.py -b BED -s SAM --extension 6 --id id + iso_name_tagging.py -b BED -s SAM --extension 6 --shift 7 --id id new name: MIMAT0002849|6|4|11M3I11M|25|CTACAAAGGGAGGTAGCACTTTCTC out SAM record: 13-1_1 0 19 44377 1 11M3I11M * 0 0 CTACAAAGGGAGGTAGCACTTTCTC * HI:i:0 MD:Z:25 NH:i:1 NM:i:3 RG:Z:A1 YZ:Z:0 YW:Z:MIMAT0002849|6|4|11M3I11M|25|CTACAAAGGGAGGTAGCACTTTCTC + explanation: + The feature's start and end coordinates are adjusted by amount of bp + specified by the CLI argument `--extension`. The alignment start and + end positions differ from the adjusted miRNA ones by 6 bp. As there is + a +/- 7 bp shift allowed and both shifts are within this range, the new + tag is added. This time using the feature ID instead of the Name. """ # noqa: E501 # pylint: enable=line-too-long @@ -129,6 +150,17 @@ def parse_arguments(): default=0, type=int, ) + parser.add_argument( + "-S", + "--shift", + help=( + "Absoulte difference in nucleotides allowed between the alignment" + " and its intersecting features' start and end coordinates." + " Default: %(default)d." + ), + default=0, + type=int, + ) parser.add_argument( "--id", help=( @@ -161,18 +193,18 @@ def parse_intersect_output( ) -> Optional[Dict[Optional[str], list]]: """Parse intersect BED file. - Given a BED file generated by intersecting a GFF file (-a) with a BAM file + Given a BED file generated by intersecting a GFF3 file (-a) with a BAM file (-b) using bedtools intersect, create a dictionary where the alignment - names are the keys. The values are lists containing the feature name, - start position, and end position. The id argument specifies the feature - name to use, and the extension argument adjusts the feature coordinates by - adding the given value and subtracts it from the end position. If the BED - file is empty, `None` is returned. + names are the keys, and the values are lists containing the feature name, + the start and the end positions. The `ID` argument specifies the feature + name to use, and the `extension` argument adjusts the feature coordinates + by adding and subtracting the given value to the start and end positions + respectively. If the BED file is empty, `None` is returned. Args: intersect_file: Path to the intersect BED file. - id: + ID: ID used to identify the feature. Defaults to "name". extension: Number of nucleotides the start and end coordinates have to be @@ -205,12 +237,12 @@ def parse_intersect_output( for line in bedfile: fields = Fields(*line.strip().split("\t")) - miRNA_name = attributes_dictionary(fields.feat_attributes)[ID] - miRNA_start = int(fields.feat_start) + extension - miRNA_end = int(fields.feat_end) - extension + feat_name = attributes_dictionary(fields.feat_attributes)[ID] + feat_start = int(fields.feat_start) + extension + feat_end = int(fields.feat_end) - extension intersect_data[fields.read_name].append( - (miRNA_name, miRNA_start, miRNA_end) + (feat_name, feat_start, feat_end) ) if not intersect_data: @@ -220,34 +252,34 @@ def parse_intersect_output( def get_tags( - intersecting_mirna: list, alignment: pysam.AlignedSegment, extend: int + intersecting_feat: list, alignment: pysam.AlignedSegment, shift: int = 0 ) -> set: - """Get tag for alignment. + """Get alignment's new tag. - Given an alignment and a list containing the name, start and end - (extended) positions of all the intersecting miRNA species, create the set - of strings used as a new custom tag to that alignment. + Given an alignment and a list containing the name, the (extended) start and + end positions of all the intersecting features, create a set of strings + to be used as a new custom tag on that alignment. Each string follows the format: - miRNA_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ + FEATURE_ID|5'-shift|3'-shift|CIGAR|MD|READ_SEQ The 5' end shift is computed as the difference between the feature and the - alignment positions. Similarly, the 3'-end shift is the result of - subtracting the feature end position to the alignment's one. If both shifts - values are within the range +/-extension, the name is added to the final - list. Note that `pysam` assumes 0-base index therefore, the addition of - one base is required to compute the 5' end shift. + alignment starting coordinate. Similarly, the 3' end shift is the result of + subtracting the feature's end position to the alignment's one. If both + shifts values are within the range +/- `shift`, the name is added to the + final list. Note that `pysam` assumes 0-base index therefore, the addition + of one base is required to compute the 5' end shift. Args: - intersecting_mirna: + intersecting_feat: list with the miRNA species name, start and end positions alignment: alignment to create the tag for - extend: + shift: value that sets the range in which both shifts have to be in to - create a new string for a particular miRNA species + create a new string for a particular feature Returns: tags: - set of strings for each valid intersecting miRNA + set of strings for each valid intersecting feature """ cigar = alignment.cigarstring seq = alignment.query_sequence @@ -255,11 +287,11 @@ def get_tags( tags = [] - for miR_name, miR_start, miR_end in intersecting_mirna: - shift_5 = alignment.reference_start - miR_start + 1 - shift_3 = alignment.reference_start + alignment.query_length - miR_end - if -extend <= shift_5 <= extend and -extend <= shift_3 <= extend: - tags.append(f"{miR_name}|{shift_5}|{shift_3}|{cigar}|{md}|{seq}") + for feat_name, feat_start, feat_end in intersecting_feat: + shift_5 = alignment.reference_start - feat_start + 1 + shift_3 = alignment.reference_start + alignment.query_length - feat_end + if -shift <= shift_5 <= shift and -shift <= shift_3 <= shift: + tags.append(f"{feat_name}|{shift_5}|{shift_3}|{cigar}|{md}|{seq}") return set(tags) @@ -280,12 +312,12 @@ def main(args) -> None: for alignment in samfile: alignment_id = alignment.query_name - intersecting_miRNAs = intersect_data[alignment_id] + intersecting_feats = intersect_data[alignment_id] tags = get_tags( - intersecting_mirna=intersecting_miRNAs, + intersecting_feat=intersecting_feats, alignment=alignment, - extend=args.extension, + shift=args.shift, ) alignment.set_tag("YW", ";".join(tags)) From e2e9bf3862838edf846647723c5168cb8a53a7d3 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 12 Jan 2025 20:16:36 +0100 Subject: [PATCH 40/42] ci: upgrade miniconda to v3 --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5ff4bf9..1951f4f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -21,7 +21,7 @@ jobs: uses: actions/checkout@v4 - name: Setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" activate-environment: mirflowz @@ -64,7 +64,7 @@ jobs: uses: actions/checkout@v4 - name: setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" activate-environment: mirflowz @@ -101,7 +101,7 @@ jobs: uses: actions/checkout@v4 - name: setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" activate-environment: mirflowz @@ -135,7 +135,7 @@ jobs: uses: actions/checkout@v4 - name: setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" activate-environment: mirflowz From 3add762ec304611128d7284f1d5fa57877979fc7 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 12 Jan 2025 20:51:22 +0100 Subject: [PATCH 41/42] ci: pin ubuntu version --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 1951f4f..785494c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -90,7 +90,7 @@ jobs: snakemake-integration-test: - runs-on: ubuntu-latest + runs-on: ubuntu-20.04 defaults: run: shell: bash -l {0} From fbf26bbd679aa61292743b3677f90ef47407a20b Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 12 Jan 2025 22:29:27 +0100 Subject: [PATCH 42/42] ci: set strict channel priority to true --- .github/workflows/tests.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 785494c..4677566 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -25,6 +25,7 @@ jobs: with: mamba-version: "*" activate-environment: mirflowz + channel-priority: true environment-file: environment.yml auto-activate-base: false @@ -68,6 +69,7 @@ jobs: with: mamba-version: "*" activate-environment: mirflowz + channel-priority: true environment-file: environment.yml auto-activate-base: false @@ -105,6 +107,7 @@ jobs: with: mamba-version: "*" activate-environment: mirflowz + channel-priority: true environment-file: environment.yml auto-activate-base: false @@ -139,6 +142,7 @@ jobs: with: mamba-version: "*" activate-environment: mirflowz + channel-priority: true environment-file: environment.yml auto-activate-base: false