Hello everyone !!
I have a question for you : I have biological replicates from Atac-seq experience and I want to perform a peak calling and then a comparison of the overlaps between my files. I have 5 samples for healthy people and 9 samples for patients and I have 2 strategies :
first, I have bam files from alignment and I merge the 5 bam for healthy together and make a second merge for the 9 samples of patients (with samtools merge) and thus I obtain 2 files (bam) and I perform peak calling on each and then search for overlap between the two sets of peaks with intersectBed
second, I have bam files from alignment (so I have a total of 14 bam files), I perform peak calling on each of the 14 samples and then I make a merge (with bedtools merge) of the 5 peak files of healthy and a second merge of the 9 peaks files of patients and then I search for overlap between the 2 sets with intersectBed.
Which one is the best strategy and why ?? Should I merge before or after the peak calling ?
Thank you in advance !!