nexus_filter_unspliced_transcripts

Filter unspliced transcripts. Transcripts that overlaps any GENCODE transcripts with only 1 exon will be retained.

Usage

nexus_filter_unspliced_transcripts \
    --bam-file /path/to/file \
    --fasta-file /path/to/file \
    --gencode-gtf-file /path/to/file.gtf \
    --output-bam-file /path/to/file.bam \
    --output-fasta-file /path/to/file.fasta \
    --output-tsv-file /path/to/file.tsv \
    [--min-mapping-quality 30] \
    [--num-processes 4]

Parameters

Parameter	Type	Default	Description
--bam-file	str	required	Input BAM file.
--fasta-file	str	required	Input FASTA file (transcriptome assembly).
--gencode-gtf-file	str	required	GENCODE GTF file.
--output-bam-file	str	required	Output BAM file.
--output-fasta-file	str	required	Output FASTA file.
--output-tsv-file	str	required	Output TSV file.
--min-mapping-quality	int	30	Minimum mapping quality (default: 30).
--num-processes	int	4	Number of processes (default: 4).