This is my notebook about how to use the pipeline from nfcore-differentialabundance https://nf-co.re/differentialabundance with nfcode-atacseq https://nf-co.re/atacseq/
The atacseq pipeline produced the following output: /results/bwa/merged_replicate/macs2/narrow_peak/consensus/consensus_peaks.mRp.clN.annotatePeaks.txt
PeakID (cmd=annotatePeaks.pl consensus_peaks.mRp.clN.bed genome.fa -gid -gtf genes.gtf -cpu 6) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation (...)
Interval_332495 chr9 124851870 124853798 + 0 NA promoter-TSS (WDR38) (...)
Interval_128586 chr17 26937319 26937399 + 0 NA Intergenic (...)