When generating models with ChromHMM for different cell types (or tissues), one of your goals might be to see which states are shared across models. ChromHMM has a solution for this with the CompareModels command, which looks at the correlation in the emission parameters for each state.

However, this command is not very useful in my opinion. Firstly, ChromHMM tells you if a state has an analagous state in a different model (not which one). Then, much more importantly, it doesn't take into account that a model might have multiple states that are very similar in terms of their emission parameters. Some of your models may have states that appear similar in emission parameters, but are spatially very different. Such states are different, but would be correlated with states in the comparison model that they shouldn't be. If you had an abundance of epigenetic datasets to work with, these states that possess similar emission parameters may start to separate to the point where spatial properties are not required to compare across models. However, an abundance of datasets is not usually feasible.

In order to solve this problem ChromCompare takes into account both the emission parameters and the spatial properties of the state's assignment on the genome. This way, users can make much more informed decisions about which states are shared between two models, and which ones are unique to only one. Knowing this information can be very useful when looking for cell type or tissue type differences.

Setup

In order to run ChromCompare, you must first complete the required setup steps highlighted below:

1. Download all required software
2. Fill in the configuration file found in .../Setup and place this file in a memorable location (you can just leave it in the Setup directory if you wish). You can also change the name of the file if you think you will have multiple configuaration files.
3. Run the main ChromCompare.sh script (found in JobSubmission) with Slurm Workload Manager, provide the full path to the config file as the first and only argument to the script.

An example of running the main script would be:

sbatch .../ChromCompare.sh .../path/to/configuration_file.txt

For additional information it is recommended that you read the documentation.

Required Software

ChromCompare requires the following software in order to run: Ensure that these software can be found on your PATH environment variable, i.e. you can run these from the command line directly (for example, conda ...).

• bash (>=4.2.46(2))
• SLURM Workload Manager (>=20.02.3)
• conda (>=v23.10.0)
• python (>= 3.10.0)
  • This should be available if you have conda installed.