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 `_emissions.txt` and `_*.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.
The `_emissions.txt` are the values that go into the `_emissions.png` figures. Each row is a state, each column is an input data file ("mark" or histone mark in the terminology of ChromHMM). Darker blue indicates a higher likelihood of finding that mark in that state. These, combined with running OverlapEnrichment with biologically meaningful datasets, are critical for figuring out how to interpret the states. 

The `segments.bed` file partitions the genome into contiguous segments, and the names of each feature in that file (E1, E2, etc) correspond to the states (1, 2, etc) in the `_emissions.png`.

A typical workflow is to figure out what to label each state. Then choose some colors and post-process the BED file with labels and names to get something more useful for downstream analysis.