Recently, I have been dealing with some H3K27me3 ChIP-seq data. I used MACS2 to callpeak (with
--broad ) and visualized the bw files (converted from bam) in IGV.
For me, this entire window seems possessed H3K27me3 modification, but the MACS2 just take the high signal region as H3K27me3 peak.
What I want to do is to get genes with H3K27me3 modification. If I take MACS2 as reference it may overlook some genes with low level H3K27me3 modification.
My question is how do yours handling this broad peak issues? Do we have better peakcallers for broad peaks like H3K27me3?
Thanks in advance