scHicNormalize¶
usage: scHicNormalize --matrix scool scHi-C matrix --outFileName OUTFILENAME
[--threads THREADS] --normalize
{smallest,read_count,multiplicative}
[--setToZeroThreshold SETTOZEROTHRESHOLD]
[--value VALUE]
[--maximumRegionToConsider MAXIMUMREGIONTOCONSIDER]
[--help] [--version]
Required arguments¶
- --matrix, -m
The single cell Hi-C interaction matrices to investigate for QC. Needs to be in scool format
- --outFileName, -o
File name of the normalized scool matrix.
- --threads, -t
Number of threads. Using the python multiprocessing module.
Default: 4
- --normalize, -n
Possible choices: smallest, read_count, multiplicative
Normalize to a) all matrices to the lowest read count of the given matrices, b) all to a given read coverage value or c) to a multiplicative value
Default: “smallest”
Optional arguments¶
- --setToZeroThreshold, -z
Values smaller as this threshold are set to 0.
Default: 1.0
- --value, -v
This value is used to either be interpreted as the desired read_count or the multiplicative value. This depends on the value for –normalize
Default: 1
- --maximumRegionToConsider
To compute the normalization factor for the normalization mode ‘smallest’ and ‘read_count’, consider only this genomic distance around the diagonal.
Default: 30000000
- --version
show program’s version number and exit