Merge pull request #437 from ncihtan/cite-seq-L1-cdna-patch

HTAN.model.csv

@@ -84,7 +84,7 @@ scmC-seq Level 2,"Files contain scmC-seq files containing aligned sequence data,
 scATAC-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATACseq Workflow Type, scATACseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scATAC-seq Level 3,,
 scDNA-seq Level 1,Single-cell DNA-seq,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Nucleic Acid Source, Library Selection Method, Read Length, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link",,FALSE,Sequencing,Biospecimen,,
 scDNA-seq Level 2,Alignment workflows downstream of scDNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads,Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Proportion Mitochondrial Reads, Contamination, Contamination Error",,FALSE,Sequencing,scDNA-seq Level 1,,
-Multiplexed CITE-seq Level 1,Raw sequencing files for the multiplexed CITE-seq assay,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source,Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method,Read Indicator, Read1, Read2, cDNA, End Bias, Reverse Transcription Primer, Spike In, Spike In Concentration, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group, Empty Well Barcode,Well Index,Feature Reference Id, Associated mRNA Library Data File ID, Single Cell Barcode Method Applied, Feature Barcode Library Type, Barcode Folder Synapse ID, Barcode Folder File List",,FALSE,Sequencing,Biospecimen,,
+Multiplexed CITE-seq Level 1,Raw sequencing files for the multiplexed CITE-seq assay,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source,Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method,Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Spike In Concentration, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group, Empty Well Barcode,Well Index,Feature Reference Id, Associated mRNA Library Data File ID, Single Cell Barcode Method Applied, Feature Barcode Library Type, Barcode Folder Synapse ID, Barcode Folder File List",,FALSE,Sequencing,Biospecimen,,
 Multiplexed CITE-seq Level 2,Alignment workflows downstream of Multiplexed CITE-seq Level 1,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Associated mRNA Library Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,Multiplexed CITE-seq Level 1,,
 Multiplexed CITE-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Associated mRNA Library Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Sequencing,scRNA-seq Level 2,,
 Multiplexed CITE-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Associated mRNA Library Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,Multiplexed CITE-seq Level 3,,

HTAN.model.jsonld

@@ -40933,9 +40933,6 @@
                 {
                     "@id": "bts:Read2"
                 },
-                {
-                    "@id": "bts:CDNA"
-                },
                 {
                     "@id": "bts:EndBias"
                 },