[Useq-users] variation between peak callers

[Noboru Jo S. <ns...@uc...>]

    Hi David, would you comment on why running different peak callers on 
the same data results in different peaks?
    I noticed that for PolII, I didn't have this problem. But for TFs 
that, I assume, have weaker enrichment, this seems to be common. I just 
ran Useq on published data and I obtained low overlap, ~20%, at 1bp. 
But, both sets make biological sense (although GO for Useq peaks/genes 
gave me fewer terms for the tissue), peaks are generally conserved, 
overrepresentation of peaks on the TSS, expression levels on the tissue 
make sense, peaks cluster as a sharp peak around the TSS.
    I always assumed that when the IP is not highly enriched, such 
variation occurs. Maybe you can say something else based on your experience?
    I mean, is this something we have to live with, or is it something 
wrong I'm doing and I should see higher overlap?
    Thanks a lot!

noboru