[Useq-users] artefactual peaks

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

     Hi David, analyzing a sample from my lab that seems to be a failed 
IP, I found a number of regions in the genome that have many reads, but 
are not real peaks. They are basically the same across samples, 
including inputs and failed IPs. One example region is mm9 
chrX:166,393,669-166,477,668 (figure attached).
     This is not a problem exclusive to USeq, but I was wondering if 
there's something that can be done to improve peak callers, since inputs 
are also "enriched" in these regions. I know that people have generated 
files containing regions that should be masked, but since input samples 
are also enriched, I wonder why they still come up as peaks.
     Thank you.