I have been trying to understand the difference between broad peaks called by macs2 and macs2.1 . I used the same parameters to call the broad peaks and I found there is a huge difference between the number of peaks that is being called. My parameters are p-value 1e-5 and broad-cutoff 0.1. I used this parameter to run on the same samples with MACS2 and MACS2.1. However I see a drastic jump in the number of peaks called with MACS2.1. Has anyone seen such a thing before? Total number of peaks in MACS2.1 is 4 times that of the number of peaks called by MACS2.0. I will try to see the overlap between the two peak files but is this a likely thing observed usually? Thanks