README.md

Dependencies:

• Local installation of java (see website for instructions)
• see chromHMM manual for instructions (http://compbio.mit.edu/ChromHMM/ChromHMM_manual.pdf)

Execution: bash learnHMM.sh

Required arguments: -chromhmm : If this flag is set, Spectacle is run exactly the same as ChromHMM as described in the ChromHMM manual (see above). -inputdir : This is the directory containing the binarized input files. Only file names containing ‘_binary’ are used by default (e.g., /BINARIZE/). -outputdir : This is the directory where the output files are written (e.g., /HMM) -numstates : This parameter specifies the number of states to include in the model (e.g., 18). -assembly : This parameter specifies the assembly. OverlapEnrichment and NeighborhoodEnrichment will be called with default parameters using this assembly (e.g., hg38).