nexus_filter_rnabloom2_transcripts

Filter RNA-Bloom2 assembled transcripts.

Usage

nexus_filter_rnabloom2_transcripts \
    --assembly4-pol-fasta-file /path/to/file.fasta \
    --assembly3-map-paf-file /path/to/file \
    [--min-mapping-quality 30] \
    [--min-read-support 3] \
    [--min-fraction-match 0.5] \
    --output-reads-tsv-file /path/to/file.tsv \
    --output-transcripts-tsv-file /path/to/file.tsv \
    --output-fasta-file /path/to/file.fasta

Parameters

Parameter	Type	Default	Description
--assembly4-pol-fasta-file	str	required	RNA-Bloom2 assembly4.pol.fa file.
--assembly3-map-paf-file	str	required	RNA-Bloom2 assembly3.map.paf.gz file.
--min-mapping-quality	int	30	Minimum mapping quality (default: 30).
--min-read-support	int	3	Minimum read support (default: 3).
--min-fraction-match	float	0.5	Minimum fraction match (default: 0.5).
--output-reads-tsv-file	str	required	Output reads TSV file.
--output-transcripts-tsv-file	str	required	Output transcripts TSV file.
--output-fasta-file	str	required	Output FASTA file.