I am trying to generate differential peaks of 2 sets of ChIP-seq experiments: cells treated with 2 different chemicals by using MACS2 bdgdiff.
I am following tips from Tao https://github.com/taoliu/MACS/wiki/Call-differential-binding-events
So first I run MACS2callpeak with input and ChIP files for each treatment.
however, after running with standard setting and also user provided setting, I keep getting back Empty results while no error has occurred. Anyone has a idea how to fix this.
thanks in advance!