Overestimate of ATAC-seq differential peaks

Question

[Darryl]

Hello

I am comparing 2 conditions of ATAC-seq. Peaks were called using MACS2, broad setting. The number of peaks in condition A is larger than condition B. However, the peaks in B are larger, and for each single peak in B there are ~2-3 smaller peaks in A. Peak height is higher in condition B, which seems to be driving that. I got similar results with narrow peak calling, which missed many features.

Thanks

[jared.andrews07]

There's no question here.