Chromatin state discovery and

characterization (original) (raw)

Note the latest version of ChromHMM will be at https://ernstlab.github.io/ChromHMM. This site is attempting to mirror its contents, but might not be at some point.

Quick instructions on running ChromHMM:
1. Install Java 1.7 or later if not already installed.
2. Unzip the file ChromHMM.zip
3. To try out ChromHMM learning a 10-state model on the sample data enter from a command line in the directory with the ChromHMM.jar file the command:

java -mx1600M -jar ChromHMM.jar LearnModel SAMPLEDATA_HG18 OUTPUTSAMPLE 10 hg18

After termination in ~5-10 minutes a file in OUTPUTSAMPLE/webpage_10.html will be created showing output images and linking to all the output files created. If a web browser is found on the computer the webpage will automatically be opened in it.
In general binarized input for the LearnModel command can be generated by first running the BinarizeBed command on bed files with coordinates of aligned reads or the BinarizeBam command on bam files with the coordinates of aligned reads.