usage: hicAdjustMatrix --matrix MATRIX --outFileName OUTFILENAME
                       [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                       [--action {keep,remove,mask}] [--regions REGIONS]
                       [--help] [--version]

Required arguments

–matrix, -m The matrix to adjust. HiCExplorer supports the following file formats: h5 (native HiCExplorer format) and cool.
–outFileName, -o
 File name to save the adjusted matrix.

Optional arguments

–chromosomes, -c
 List of chromosomes to keep / remove

Possible choices: keep, remove, mask

Keep, remove or mask the list of specified chromosomes / regions

Default: “keep”

–regions, -r BED file which stores a list of regions to keep / remove
–version show program’s version number and exit

hicAdjustMatrix can mask, remove or keep defined regions from a BED file or given chromosomes.

Example usages

$ hicAdjustMatrix -m matrix.cool --action keep --chromosomes chr1 -o matrix_chr1.cool
$ hicAdjustMatrix -m matrix.cool --action mask --regions mask_regions.bed -o matrix_masked.cool


chr1    10  30
chr1    50  300