Call peaks in replicates

[Kevinckyy]

Hello! I'm wondering why there is no way to use two or more bam files as treat/control to call peaks, just like what we can do in macs2 by writing multiple files following the parameter -t and -c.

Just like this:

macs2 callpeak -t t1.bam t2.bam -c c1.bam c2.bam

It's a very common requirement, could you please add this function?

[gartician]

Hi @Kevinckyy,

While I am not familiar with that feature in MACS2, could you in practice concatenate the BAM files together before calling peaks?