scHicQualityControl

usage: scHicQualityControl --matrix scool scHi-C matrix
                           [--outputScool OUTPUTSCOOL]
                           [--minimumReadCoverage MINIMUMREADCOVERAGE]
                           [--minimumDensity MINIMUMDENSITY]
                           [--maximumRegionToConsider MAXIMUMREGIONTOCONSIDER]
                           [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                           [--outFileNameDensity OUTFILENAMEDENSITY]
                           [--outFileNameReadCoverage OUTFILENAMEREADCOVERAGE]
                           [--outFileNameQCReport OUTFILENAMEQCREPORT]
                           [--plotOnly] [--runChromosomeCheck] [--dpi DPI]
                           [--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

Optional arguments

--outputScool, -o

scool matrix which contains only the filtered matrices

Default: “filtered_matrices.scool”

--minimumReadCoverage

Remove all samples with a lower read coverage as this value.

Default: 1000000

--minimumDensity

Remove all samples with a lower density as this value. The density is given by: number of non-zero interactions / all possible interactions.

Default: 0.001

--maximumRegionToConsider

To compute the density, consider only this genomic distance around the diagonal.

Default: 30000000

--chromosomes, -c

List of chromosomes that a cell needs to have to be not deleted. However, other chromosomes/contigs and scaffolds which may exist are not deleted. Use scHicAdjustMatrix for this.

--outFileNameDensity, -od

File name of the density histogram

Default: “density.png”

--outFileNameReadCoverage, -or

File name of the read coverage

Default: “readCoverage.png”

--outFileNameQCReport, -oqc

File name of the quality report

Default: “qc_report.txt”

--plotOnly

Do not create a new matrix, create only the plots.

Default: False

--runChromosomeCheck

Skip the data integrity check for the chromosomes.

Default: False

--dpi, -d

The dpi of the plot.

Default: 300

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--version

show program’s version number and exit