nexus_count_scrna_assembly_support

Count cell and molecule support for each transcript from assembled from scRNA-seq.

Usage

nexus_count_scrna_assembly_support \
    --fasta-file /path/to/file \
    --bam-file /path/to/file \
    --reads-tsv-file /path/to/file.tsv \
    --output-tsv-file /path/to/file.tsv \
    [--tag CB]

Parameters

Parameter	Type	Default	Description
--fasta-file	str	required	Transcriptome assembly FASTA file.
--bam-file	str	required	Unaligned BAM file.
--reads-tsv-file	str	required	Reads TSV file (expected columns: ‘transcript_id’, ‘read_name’).
--output-tsv-file	str	required	Output TSV file.
--tag	str	CB	Cell barcode tag in the BAM file (default: ‘CB’).