scHicAdjustMatrix

scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the scool file.

usage: scHicAdjustMatrix --matrix MATRIX --outFileName OUTFILENAME
                         [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                         [--createSubmatrix CREATESUBMATRIX]
                         [--action {keep,remove}] [--threads THREADS] [--help]
                         [--version]

Required arguments

--matrix, -m

The matrix to adjust in the scool format.

--outFileName, -o

File name to save the adjusted matrix.

Optional arguments

--chromosomes, -c

List of chromosomes to keep / remove

--createSubmatrix, -cs

Keep only first n matrices and remove the rest. Good for test data creation.

--action

Possible choices: keep, remove

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

Default: “keep”

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--version

show program’s version number and exit