I have a H3K27me3 bed file that is predicted by SICER and H3K4me3 narrowPeak file predicted by MACS2.
I want to know what are those monovalent promoter(that is with only one mark in the promoter region)
This is what I did:
1.I use bedtools to find the H3K4me3 summits that has no overlap with H3K27me3 broad peaks(bedtools intersect -v)
2.Then I find the overlap between step 1 result and the slopped annotation bed file that have the coordinate from -500 bp and +500 bp of TSS of genes
3.Similar to step 1 & 2, I try to find the promoter that only marked by H3K27me3 broad peaks
Here is what I got: The result of monovalent promoter of H3K4me3 seems good and reasonable, while the result of H3K27me3 is not quit good. I got many results that H3K27me3 peaks spread across gene body but not in the promoter region. (I check various transcript and it seems that there are no H3K27me3 peaks that fall in promoter region).
Any hints about this?
Thanks a lot !