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NAME¶
ChromHMM - Learning and analysis chromatin states using a multivariate Hidden
Markov Model
SYNOPSIS¶
java -Xmx[GB]g -jar /usr/share/java/chromhmm.jar [options]
DESCRIPTION¶
ChromHMM is software for learning and characterizing chromatin states. ChromHMM
can integrate multiple chromatin datasets such as ChIP-seq data of various
histone modifications to discover de novo the major re-occuring combinatorial
and spatial patterns of marks. ChromHMM is based on a multivariate Hidden
Markov Model that explicitly models the presence or absence of each chromatin
mark. The resulting model can then be used to systematically annotate a genome
in one or more cell types. By automatically computing state enrichments for
large-scale functional and annotation datasets ChromHMM facilitates the
biological characterization of each state. ChromHMM also produces files with
genome-wide maps of chromatin state annotations that can be directly
visualized in a genome browser.
OPTIONS¶
- 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.
- BinarizeBed
- Converts a set of bed files of aligned reads into binarized data files for
model learning and optionally prints the intermediate signal files.
- BinarizeBam
- Converts a set of bam files of aligned reads into binarized data files for
model learning and optionally prints the intermediate signal files.
- BinarizeSignal
- Converts a set of signal files into binarized files.
- MakeSegmentation
- Takes a learned model and binarized data and outputs a segmentation.
- MakeBrowserFiles
- Can convert segmentation files into a browser viewable format.
- OverlapEnrichment
- Shows the enrichment of each state of a segmentation for a set of external
data.
- NeighborhoodEnrichment
- Shows the enrichment of each state relative to a set of anchor positions.
- CompareModels
- Can compare models with different numbers of states in terms of
correlation in emission parameters.
- Reorder
- Allows reordering the states of the model, the columns of the emission
matrix, or adding state labels.
- EvalSubset
- Can be used to evaluate the extent to which a subset of marks can recover
a segmentation using the full set of marks.
- StatePruning
- Can be used to prune states from a model in order to initialize models
when using the non-default two pass approach.
AUTHOR¶
ChromHMM was written by Jason Ernst.
