build-transcriptome-var-graph

Build a transcriptome variation graph.

Usage

Template:

exacto build-transcriptome-var-graph \
    --transcript-structures-tsv-file <transcript_structures_tsv_file> \
    --fasta-file <fasta_file> \
    --output-fasta-file <output_fasta_file> \
    [--graph-type GRAPH_TYPE] \
    [--num-threads NUM_THREADS] \
    [--batch-size BATCH_SIZE]

Example:

exacto build-transcriptome-var-graph \
    --transcript-structures-tsv-file tumor_primary_structures.tsv \
    --fasta-file reference_transcriptome.fasta \
    --output-fasta-file transcriptome_var_graph.fasta

Description

Build a transcriptome variation graph.

At a glance

Inputs: *.tsv (transcript structures), *.fasta (reference transcriptome)

Outputs: *.fasta (transcriptome variation graph)

Typical next step: Endpoint — feeds downstream graph-aware analyses

Required arguments

Flag	Type	Description
`--transcript-structures-tsv-file`	`str`	Transcript structures TSV file. Expected columns: ‘transcript_model_id’, ‘index’, ‘chromosome_1’, ‘position_1’, ‘operation_1’, ‘strand_1’, ‘chromosome_2’, ‘position_2’, ‘operation_2’, ‘strand_2’, ‘sequence’, ‘num_cycles’.
`--fasta-file`	`str`	Reference genome FASTA file (variation graph backbone).
`--output-fasta-file`	`str`	Output FASTA file.

Optional arguments

Flag	Type	Default	Description
`--graph-type`	`str`	`individual`	Variation graph type. Either ‘individual’ or ‘population’.
`--num-threads`	`int`	`4`	Number of threads.
`--batch-size`	`int`	`1000`	Batch size.