hicAdjustMatrix¶
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 Hi-C 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¶
- --action
Possible choices: keep, remove, mask
Keep, remove or mask the list of specified chromosomes / regions.
Default: “keep”
- --version
show program’s version number and exit
hicAdjustMatrix can mask, remove or keep defined regions from a BED file or given chromosomes. This can be useful to create a smaller Hi-C matrix of a single chromosome for e.g. testing purposes or to remove repetitive chromosome ends before calculating A/B compartments using hicPCA.
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
mask_regions.bed
chr1 10 30
chr1 50 300