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).

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

Input/Output options

--input, -i

sincei-generated 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 file 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.

--region_blacklist, -rb

A BED or GTF file containing regions that should be excluded from all analyses. Regions in the anndata object that overlap with blacklisted regions will be removed.

--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 space separated list of chromosomes to exclude. eg. chrM chrUn

Other options

--verbose, -v

Set to see processing messages.

-V, --version

Print the program version and exit.