remove-unspliced-rnas

Remove unspliced RNAs.

Usage

Template:

exacto remove-unspliced-rnas \
    --bam-file <bam_file> \
    --bam-bai-file <bam_bai_file> \
    --fasta-file <fasta_file> \
    --reference-gene-annotation-file <reference_gene_annotation_file> \
    --reference-gene-annotation-source <reference_gene_annotation_source> \
    --reference-gene-annotation-assembly <reference_gene_annotation_assembly> \
    --reference-gene-annotation-version <reference_gene_annotation_version> \
    --output-bam-file <output_bam_file> \
    --output-bam-bai-file <output_bam_bai_file> \
    --output-fasta-file <output_fasta_file> \
    [--num-threads NUM_THREADS] \
    [--min-mapping-quality MIN_MAPPING_QUALITY] \
    [--gene-types GENE_TYPES [GENE_TYPES ...]] \
    [--gene-levels GENE_LEVELS [GENE_LEVELS ...]] \
    [--transcript-types TRANSCRIPT_TYPES [TRANSCRIPT_TYPES ...]] \
    [--transcript-levels TRANSCRIPT_LEVELS [TRANSCRIPT_LEVELS ...]]

Example:

exacto remove-unspliced-rnas \
    --bam-file tumor_transcriptome_assembly.sorted.bam \
    --bam-bai-file tumor_transcriptome_assembly.sorted.bam.bai \
    --fasta-file reference_genome.fasta \
    --reference-gene-annotation-file gencode.gtf.gz \
    --reference-gene-annotation-source gencode \
    --reference-gene-annotation-assembly hg38 \
    --reference-gene-annotation-version v44 \
    --output-bam-file tumor_transcriptome_assembly.sorted.filtered.bam \
    --output-bam-bai-file tumor_transcriptome_assembly.sorted.filtered.bam.bai \
    --output-fasta-file tumor_transcriptome_assembly.sorted.filtered.fasta

Description

Remove unspliced RNAs.

At a glance

Inputs: *.bam, *.bam.bai, *.fasta, *.gtf.gz

Outputs: Filtered *.bam, *.bam.bai, *.fasta

Typical next step: call-rna-vars

Required arguments

Flag	Type	Description
`--bam-file`	`str`	Input BAM file of assembled transcripts.
`--bam-bai-file`	`str`	Input BAM.BAI file of assembled transcripts.
`--fasta-file`	`str`	Input FASTA file of assembled transcripts.
`--reference-gene-annotation-file`	`str`	Reference gene annotation file.
`--reference-gene-annotation-source`	`str`	Reference gene annotation source.
`--reference-gene-annotation-assembly`	`str`	Reference gene annotation assembly (e.g. ‘hg38’).
`--reference-gene-annotation-version`	`str`	Reference gene annotation version (e.g. ‘v41’).
`--output-bam-file`	`str`	Output BAM file.
`--output-bam-bai-file`	`str`	Output BAM file.
`--output-fasta-file`	`str`	Output FASTA file.

Optional arguments

Flag	Type	Default	Description
`--num-threads`	`int`	`4`	Number of threads.
`--min-mapping-quality`	`int`	`30`	Minimum mapping quality.
`--gene-types`	`str`	`protein_coding`	Reference gene types to include in annotation.
`--gene-levels`	`int`	`1, 2`	Reference gene levels to include in annotation.
`--transcript-types`	`str`	`protein_coding`	Reference transcript types to include in annotation.
`--transcript-levels`	`int`	`1, 2`	Reference transcript levels to include in annotation.