MACS2 peak caller omitting large chunks of peaks
Hi all,
We performed ATAC-seq on a cell line for which we got about 100,000 peaks using MACS2 peak caller. However, in some of the chromosomes there were very few or no peaks called at all. Is this normal? Would we reasonable expect that there would be similar number of peaks called across the different chromosomes. What could potentially be wrong?
Many thanks in advance!
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Nevergivingup •
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Given the different size of chromosomes (in human chr22 is about 1/5th of the size of chr1), I do not see how the assumption of equal peak numbers per chromosome would hold true, or why this would be assumed in the first place.
So what is the issue here? Do you see peaks on the IGV that macs2 does not call or are you more like wondering why some regions or chromosomes have few peaks? Can you add numbers to back that up?