Description

Peak-calling for ChIP-seq and ATAC-seq enrichment experiments

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

treatment_bam (file)

Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates

*.{bam,sam}

control_bam (file)

Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples

*.{bam,sam}

blacklist_bed (file)

Bed file containing genomic intervals to exclude from the analysis

*.{bed}

save_pvalues (boolean)

Create bedgraph-ish file for p/q-values file

save_pileup (boolean)

Create bedgraph-ish file for pileups and p-values

save_bed (boolean)

Create BED file for reads/fragments/intervals

save_duplicates (boolean)

Create PCR duplicates file (only works if -r option is set)

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

peaks (file)

Output file is in ENCODE narrowPeak format

*.{narrowPeak}

bedgraph_pvalues (file)

bedGraph file containing p/q values

*.{pvalues.bedGraph}

bedgraph_pileup (file)

bedGraph file containing pileups and p-values

*.{pileup.bedGraph}

bed_intervals (file)

Bed file containing annotated intervals

*.{intervals.bed}

duplicates (file)

Text output file containing intervals corresponding to PCR duplicates

*.{intervals.txt}

version (file)

File containing software version

*.{version.txt}
maintainers
Github user JoseEspinosa
Github user samuelruizperez
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

genrich
MIT

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

github.com/jsh58/Genrich github.com/jsh58/Genrich#readme https://github.com/jsh58/Genrich