nexus_filter_scrna_assembly

Filter scRNA-seq assembly based on minimum cell and molecule support.

Usage

nexus_filter_scrna_assembly \
    --fasta-file /path/to/file \
    --support-tsv-file /path/to/file.tsv \
    --min-cells 0 \
    --min-molecules 0 \
    --output-fasta-file /path/to/file.fasta \
    --output-tsv-file /path/to/file.tsv

Parameters

Parameter	Type	Default	Description
--fasta-file	str	required	Transcriptome assembly FASTA file.
--support-tsv-file	str	required	Support TSV file (expected columns: ‘transcript_id’, ‘num_molecules’, ‘num_cells’).
--min-cells	int	required	Minimum cell count.
--min-molecules	int	required	Minimum molecule count.
--output-fasta-file	str	required	Output FASTA file.
--output-tsv-file	str	required	Output TSV file.