- chromhmm chromhmm-learnmodel
takes a set of binarized data files, learns chromatin state models, and by default produces a segmentation, generates browser output with default settings, and calls OverlapEnrichment and NeighborhoodEnrichments with default settings for the specified genome assembly. A webpage is a created with links to all the files and images created.
- chromhmm chromhmm-binarizebed
converts a set of bed files of aligned reads into binarized data files for model learning and optionally prints the intermediate signal files