see config.yaml for an example.
Reference name, this is the name that will be used as the genome name in the UCSC track hub, so be sure to use a valid UCSC genome name when possible.
ref_name: hg38
Reference fasta file:
ref: /path/to/hg38.fa
Manifest of input sample(s), must have two white-space separated columns: sample name (sample) and input bam file path (bam). See config.tbl for an example. The bam file must be indexed and aligned to the reference genome in the ref option.
manifest: config/config.tbl
Max number of threads to use in very distributed steps:
max_t: 4
Filter peaks that are more than x standard deviations from the mean coverage:
coverage_within_n_sd: 5
Exclude the following regions when creating a null distribution of FIRE scores. This is not needed if your reference is hg38 as the defaults will automatically load!
excludes:
- annotations/gaps.bed
- annotations/centromeres.bed
- annotations/cnvs.bed
Reference contigs smaller than this length are skipped by the FIRE pipeline. Default is 0.
min_contig_length: 0
Min coverage of FIRE elements for calling a FIRE peak. Default is 4.
min_coverage: 4
Forgo the use of FDR peak calling and instead call peaks for regions with at least this fraction of reads actuated. Default is 0.0 for no filter.
min_per_acc_peak = 0.25
Apply a percent actuation filter on top of the FDR peak calling. Default is 0.0 for no filter.
min_frac_accessible: 0.0
Process only chromosomes matching this regular expression:
keep_chromosomes: "chr[0-9XY]+$"
The false discovery rate (FDR) for calling FIRE peaks. Default is 0.05.
max_peak_fdr: 0.05
The allowed false discovery rate for calling individual FIRE elements. Default is 0.10.
min_fire_fdr: 0.10
The minimum number of MSPs in a Fiber-seq read for it to be included in the analysis. Default is 10.
min_msp: 10
The minimum average size of MSPs in a Fiber-seq read for it to be included in the analysis. Default is 10.
min_ave_msp_size: 10