scHicMergeMatrixBins

Merges bins from a Hi-C matrix. For example, using a matrix containing 5kb bins, a matrix of 50kb bins can be derived using –numBins 10.

usage: scHicMergeMatrixBins --matrix matrix.scool --outFileName OUTFILENAME
                            --numBins int [--runningWindow]
                            [--threads THREADS] [--help] [--version]

Required arguments

--matrix, -m

Matrix to reduce in scool format.

--outFileName, -o

File name to save the resulting matrix. The output is also a .scool file. But don’t add the suffix.

--numBins, -nb

Number of bins to merge.

Optional arguments

--runningWindow

set to merge for using a running window of length –numBins. Must be an odd number.

Default: False

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--version

show program’s version number and exit