Comparing open chromatin data to ChromHMM model
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.
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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.
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GouthamAtla
You can check chromatin states in mouse. For example, I found one quickly here from mouse ENCODE.
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GouthamAtla
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