Associating histone enriched regions with genomic features

[bhdavis1978]

Hello everyone,

I was wondering how others go about associating regions of histone enrichment with genomic features (e.g. genes, exons, tsp, etc). In some cases (for e.g. H3K36me3) it's quite easy, but for others it's less clear to me. Does anyone have any advice, or better yet references where I can read about how others have handled the situation. It seems like it must be quite a common problem, I just haven't had any luck finding any discussions of it.

Thanks

[kalyankpy]

You may get fine tuned answers if you could let the community know what is the environment you are familiar with. For eg., Are you looking for annotation tools in R or PERL or commandline based tools!

[bhdavis1978]

I'm using R and I've found ChIPpeakAnno, but I was looking more for a set of references describing the rationale of how people have gone about annotating epigenetic features. Things like H3K4me3, H3K27ac, and H3K36me3 are pretty obvious, but in the case of distal enhancers it's less obvious to me, since the effects can be over 100kb.