I have a ChIP-Seq data from multiple histone marks (H3K9me3, H3K27me3, H3K27ac and so on..(n=10)). I want to identify enrichment of these histone marks at genomic features: eg. promoter, gene body, and custom bins of n bp. So that I can correlate this data with differentially expressed genes and confer if the behaviour of histone marks profile influence gene expression. If you can suggest a R package/Tool which can do this entirely it will be the best option.
Here are the approaches I am following:
- Using the bam files of histone marks to predict chromatin state using ChromHMM and overlapping with genomic features to identify those regions which overlap with various chromatin state (the bed file have coordinates of 200 bp span of chromatin states). This approach seems ok but a same promoter coordinate overlaps with multiple chromatin states and it is difficult to determine the exact state of the particular promoter region.
- Using the bam files and gene or promoter coordinates, I created a table that contains depth normalized counts. But from this table how to say which histone mark is abundant than the other and directly reflects a particular chromatin state.
I would appreciate any help.