Hi All, I am analyzing Chip Seq data generated with 6 different antibodies: H3K4me3 H3K27ac H3K4me1 H3K27me3 H3K9me3 H3K36me3
I used macs2 for peak calling and DiffBind for differential bound sites between the subtypes of a cancer. Now I want to see the status for these histones around my genes of interest. Since many of these are enriched for enhancer and promoter regions, I am not sure which genomic coordinates I should consider in order to check their status around the genes of my interest.
I have read somewhere to consider +-10 Kb window around the TSS. I guess this could be fine for the peaks that have diffuse signal (like H3K9me1 and H3K27me3) but what is best for the narrow peaks?
I know H3K36me3 is highly enriched in intragenic regions, does that mean I should check for this in the CDS?
Any recommendations will be highly appreciated.