Can someone please help me to understand why for ChIP-seq we should not merge the biological replicates before peak calling. I read in several papers, peaks calling is done on individual replicates. I am struggling to understand this. Ideally if I merge replicates I should have more power, means more coverage in peak regions.
My results also indicates that if I call peaks on individual replicates, I get around 10,000 peaks in each rep. I have 3 replicates for chip and 3 for control. If I merge these together and run macs2, I get very few peaks < 100. Can anyone please explain this.