Comparing open chromatin data to ChromHMM model

Question

[rbronste]

Hi, curious about the best way to go about seeing where ATAC-seq peaks fall in a ChromHMM state model of a number of histone marks and TFs? To build a model pulled GEO data for marks and TFs from papers and would like to compare to our ATAC data. Thanks.

Answer 1

[GouthamAtla]

Is it human data ? Check different chromatin states from epigenome roadmap for various tissues. You can represent the enichments of ATAC peak in various regulatory elements.

[rbronste]

No this is actually mouse data.

[GouthamAtla]

You can check chromatin states in mouse. For example, I found one quickly here from mouse ENCODE.