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