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!