scHicConsensusMatrices

scHicConsensusMatrices creates based on the clustered samples one consensus matrix for each cluster. The consensus matrices are normalized to an equal read coverage level and are stored all in one scool matrix.

usage: scHicConsensusMatrices --matrix scool scHi-C matrix --clusters cluster
                              file --outFileName OUTFILENAME
                              [--no_normalization] [--threads THREADS]
                              [--help] [--version]

Required arguments

--matrix, -m

The single cell Hi-C interaction matrices to investigate for QC. Needs to be in scool format

--clusters, -c

Text file which contains per matrix the associated cluster.

--outFileName, -o

File name of the consensus scool matrix.

Optional arguments

--no_normalization

Do not plot a header.

Default: True

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--version

show program’s version number and exit