Promoter or enhancer regions in ATAC-seq data

[tamadp]

Hey,
I have used MACS to find the peaks on 2 atac-seq samples (control and treatment). From there, I have binned the peaks in regions, and counted how many peaks each sample has in each region, and taken the regions with highest peak density difference between samples to further analise them.

What I would like to do know is check the histone marks for those regions to try to identify enhancers that may be involved in differential gene expression between both samples. Is there any tool available to do this kind of annotation?

[atpoint]

The most straight-forward way would be to check the literature if there are ChIP-seq data available for the specific histone marks in your cell type AND! for the conditions you kept them.

If so, either download them from the NCBI omnibus and run the typical ChIP-seq analysis or download (if available) just the peak files. Then you can use tools like bedtools intersect to check for overlaps between the open chromatin regions and the ChIP-seq tracks.