Question

Comparing open chromatin data to ChromHMM model

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6.8 years ago

rbronste ▴ 420

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.

chromHMM ChIP-Seq ATAC-seq • 2.6k views

ADD COMMENT • link updated 6.7 years ago by Biostar 20 • written 6.8 years ago by rbronste ▴ 420

score 0 · Answer 1 · 2017-08-05

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6.7 years ago

GouthamAtla 12k

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.

ADD COMMENT • link 6.7 years ago by GouthamAtla 12k

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No this is actually mouse data.

ADD REPLY • link 6.7 years ago by rbronste ▴ 420

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

ADD REPLY • link 6.7 years ago by GouthamAtla 12k