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