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