How to get the pooled-replicate narrowPeak file for IDR peak-list
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3.3 years ago
ben.kunfang ▴ 30


I am newbie for peak calling. When I am trying to follow ENCODE's pipeline to merge narrowPeak from replicates, I stuck with this pooled-replicate narrowPeak file to run IDR. I check the IDR github and it says "Run idr using an oracle peak list (e.g. peaks called from merged replicates)", which seems the pooled-replicates narrowPeak is merging the bam file first and then use macs2 to call peaks. But I am not sure what is the control file for the merged bam file? Should I merged two replicate control file to get the control file?

Or this pooled replicate is just simply merged the narrowPeak files from replicates.

Thanks a lot!

IDR pooled-replicate • 1.3k views

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