Question: ChromHMM: chromatin states to genome % coverage?
gravatar for Sy80
3.4 years ago by
United States
Sy800 wrote:

Hi all,

I'm trying to wrap my head around ChromHMM. short version: I can't gather from the ChromHMM/ENCODE papers how one goes from chromatin state to % genome coverage of states across different cell lines?

long version: We have three conditions (wild-type, het, ko cells) with 6 histone mark ChIP-seq data per condition.

We are trying to create a joint model using all the data (18 histone marks total) from our peak calls and then use the jointly learned chromatin states to determine genome coverage per chromatin state for our 3 conditions (to determine similarities/differences between conditions).

First, we merged all our peaks (each histone mark separately) for all conditions and created a virtual chromosome per histone mark and used this virtual genome to learn a 12-state model.

My question is, how can we use the joint chromatin states to get genome coverage per state and per cell line separately??

Hope my question was clear...I appreciate any input. Thanks!

chromhmm chip-seq • 1.5k views
ADD COMMENTlink modified 14 months ago by Researcher60 • written 3.4 years ago by Sy800

Hi @Sy80, Even I am looking for answer to my similar question. Was just curious to ask were you able to get it done. I'll appreciate if you can share your experience here and the strategy you followed to get this done.


ADD REPLYlink modified 14 months ago • written 14 months ago by Researcher60

If you set up your tissue marks file to define each cell line separately, then ChromHMM should have produced segmentation files specific for each cell line. There should also be a file called CellLine_12_coverage.txt for each cell line, which has a genome coverage column.

ADD REPLYlink written 13 months ago by colin.kern920
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