nexus_find_scrna_barcode_knee

Find the knee of the barcode rank plot from an unaligned scRNA-seq BAM file.

Usage

nexus_find_scrna_barcode_knee \
    --bam-file /path/to/file \
    [--tag CB] \
    [--percentile 99] \
    [--multiplier 0.1] \
    --output-tsv-file /path/to/file.tsv \
    --output-png-file /path/to/file \
    [--num-threads 4]

Parameters

Parameter	Type	Default	Description
--bam-file	str	required	Input BAM file (unaligned).
--tag	str	CB	Cell barcode tag (default: ‘CB’).
--percentile	float	99	Percentile method’s percentile to determine the knee (default: 99’).
--multiplier	float	0.1	Percentile method’s multiplier to determine the knee (default: 0.1’).
--output-tsv-file	str	required	Output TSV file.
--output-png-file	str	required	Output PNG file. If you specify this, the plot will not be shown via the terminal.
--num-threads	int	4	Number of threads (default: 4).