scCountQC

scCountQC calculates multiple quality controls metrics on the input .h5ad file (output of scCountReads) and (optionally) filters the input file based on filterCellArgs/filterRegionArgs. The output is either an updated .h5ad object (if filtering is requested) or the filtering metrics (--outMetrics) and plots (--outPlot).

usage: scCountQC -i cellCounts.h5ad -o qc_metrics.tsv

Input/Output options

--input, -i

Input file in .h5ad format.

--outFile, -o

The file to write results to. For scFilterStats, scFilterBarcodes and scJSD, the output file is a .tsv file. For other tools, the output file is an updated .h5ad object with the result of the requested operation.

Filtering arguments

--describe, -d

Print a list of cell and region metrics available for QC/filtering.

--outMetrics, -om

Prefix of the output file with calculated QC metrics. If given, the cell metrics are printed in <prefix>.cell.tsv and region metrics as <prefix>.region.tsv

--filterCellArgs, -fc

List of arguments to filter cells. The format is "arg_name: minvalue, maxvalue; arg_name: minvalue, maxvalue; ...." where arg_name is the QC metric for cells present in the input h5ad file. In order to view all available cell filtering metrics, run scCountFilter with "--describe". The two arguments are supplied (minvalue, maxvalue) they are used as lower and upper bounds to filter cells. Make sure they are float/integer numbers.

--filterRegionArgs, -fr

List of arguments to filter regions. The format is "arg_name: minvalue, maxvalue; arg_name: minvalue; ...." where arg_name is the QC metric for regions present in the input h5ad file. In order to view all available cell filtering metrics, run scCountFilter with "--describe". The two arguments are supplied (minvalue, maxvalue) they are used as lower and upper bounds to filter cells. Make sure they are float/integer numbers.

--cell_blacklist, -cb

A list of barcodes to be excluded for the clustering. The barcodes (along with sample labels) must be present in the input object.

--chrom_blacklist, -chb

A comma separated list of chromosomes to exclude. eg. chrM, chrUn

Plot options

--plotWidth

Output plot width (in cm). (Default: 10)

--plotHeight

Output plot height (in cm). (Default: 10)

--plotFileFormat

Possible choices: png, pdf, svg, eps

Image format type. If given, this option overrides the image format based on the plotFile ending. (Default: 'png')

Other options

--verbose, -v

Set to see processing messages.

--version

show program's version number and exit