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