scHicManageScool¶
This script offers methods to extract cool files or to update a scool file for scHiCExplorer version 5
usage: scHicManageScool --matrix MATRIX --outFileName OUTFILENAME
[--action {update,extractToCool,extractScool}]
[--cellList CELLLIST] [--threads THREADS] [--help]
[--version]
Required arguments¶
- --matrix, -m
The scool matrix
- --outFileName, -o
File name to save the exported matrix, in case of extract the folder name
Optional arguments¶
- --action, -a
Possible choices: update, extractToCool, extractScool
The different actions this tool is able to do. Update can be used to update scool files from scHiCExplorer version 4 to the file format as it is used starting from scHiCExplorer 5.ExtractToCool extracts either a given scool file to individual cool files or only a subset given by a list. ExtractScool requires a list of internal cells that should be copied to a new scool file.
Default: “none”
- --cellList, -cl
A text file with the cells that should be extracted or copied to the a new scool file.
- --threads, -t
Number of threads. Using the python multiprocessing module.
Default: 4
- --version
show program’s version number and exit