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!