Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
meta
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
treatment_bam
Coordinate sorted BAM/SAM file from treatment sample
*.{bam,sam}
control_bam
Coordinate sorted BAM/SAM file from control sample
blacklist_bed
Bed file containing genomic intervals to exclude from the analysis
*.{bed}
save_pvalues
Create bedgraph-ish file for p/q-values file
save_pileup
Create bedgraph-ish file for pileups and p-values
save_bed
Create BED file for reads/fragments/intervals
save_duplicates
Create PCR duplicates file (only works if -r option is set)
peaks
Output file is in ENCODE narrowPeak format
*.{narrowPeak}
bedgraph_pvalues
bedGraph file containing p/q values
*.{pvalues.bedGraph}
bedgraph_pileup
bedGraph file containing pileups and p-values
*.{pileup.bedGraph}
bed_intervals
Bed file containing annotated intervals
*.{intervals.bed}
duplicates
Text output file containing intervals corresponding to PCR duplicates
*.{intervals.txt}
version
File containing software version
*.{version.txt}
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.
