scHicConvertFormat

scHicConvertFormat is a tool to convert a scool matrix to other single-cell Hi-C formats. So far only the structure of scHiCluster is supported: https://github.com/zhoujt1994/scHiCluster

usage: scHicConvertFormat --matrix MATRIX --outputFolder OUTPUTFOLDER
                          [--outputCellNameFile OUTPUTCELLNAMEFILE]
                          [--outputChromosomeSize OUTPUTCHROMOSOMESIZE]
                          [--format {schicluster,sparse-matrix-files}]
                          [--threads THREADS] [--help] [--version]

Required arguments

--matrix, -m

The matrix to adjust in the scool format.

--outputFolder, -of

Folder name to save the files

Default: “.”

--outputCellNameFile, -oc

File name to save the cell names and their location

Default: “cellNameFile.txt”

--outputChromosomeSize, -os

File name to save the chromosome sizes

Default: “chromosomeSize.txt”

Optional arguments

--format, -f

Possible choices: schicluster, sparse-matrix-files

The format of the output files

Default: “schicluster”

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--version

show program’s version number and exit