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

Named Arguments

--chromosomes, -c

List of chromosomes to keep / remove

--regions, -r

BED file which stores a list of regions to keep / remove

--maskBadRegions, -mbr

Bad regions are identified and masked.

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


Possible choices: keep, remove, mask

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

Default: “keep”


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