I am a first year PhD student and I have started working with 450k data recently.
I would like to use ENCODE data to check the overlap of all the available histone marks with our significantly methylated 450k array probes. We are trying to find which histone marks are most prevalent at those DNA sites where we see methylation differences. I was wondering if there are any tools available to do this. I have used ggbio, Annotationhub, but I was able to check only few types of histone markers. I appreciate any suggestions or tips.
Thanks for your time.