I've been doing some work that involves characterizing potential chromatin states in a HCT116 cell model. I've successfully been able to run
ChromHMM to identify chromatin states using a variety of histone markers and then overlap them with other datasets in order to double-check their annotation.
However, I am having a problem understanding some of the output files that
ChromHMM automatically generates. Specifically
_*.bed. I know there's a couple of people here that are really familiar with the software and could probably help me out.
I have already searched google, and read the ChromHMM manuscript, but neither provided answers.