scCountQC

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

usage: Example usage: scCountQC -i cellCounts.loom -om qc_metrics.tsv > log.txt

Input/Output options

--input, -i

Input file in .loom format

--outFile, -o

The file to write results to. For scFilterStats, scFilterBarcodes and scJSD, the output file is a .txt file. For other tools, the output file is an updated .loom 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 loom 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 loom 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 included 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