nexus_convert_scrna_bam2fastq

Convert an unaligned BAM file to a FASTQ.GZ file while filtering for barcodes with sufficient reads.

Usage

nexus_convert_scrna_bam2fastq \
    --bam-file /path/to/file \
    --barcode-tag "" \
    --output-fastq-file /path/to/file.fastq \
    --output-tsv-file /path/to/file.tsv \
    --min-reads-per-barcode 0 \
    [--base-quality 60] \
    [--num-threads 4]

Parameters

Parameter	Type	Default	Description
--bam-file	str	required	BAM file. Make sure this is an unaligned BAM file.
--barcode-tag	str	required	Barcode tag (e.g. CB for PacBio single-cell RNA-seq BAM file).
--output-fastq-file	str	required	Output FASTQ.GZ file.
--output-tsv-file	str	required	Output TSV file.
--min-reads-per-barcode	int	required	Minimum number of reads per barcode. Determine this value by running nexus_find_scrna_barcode_knee.
--base-quality	int	60	Default base quality score to use when reads lack quality scores (default: 60).
--num-threads	int	4	Number of threads (default: 4).