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