determine-rna-consensus

Determine an RNA consensus sequence for each RNA read cluster.

Usage

Template:

exacto determine-rna-consensus \
    --tsv-file <tsv_file> \
    --fastq-file <fastq_file> \
    --output-dir <output_dir> \
    --output-prefix <output_prefix> \
    [--match-score MATCH_SCORE] \
    [--mismatch-score MISMATCH_SCORE] \
    [--gap-open-score GAP_OPEN_SCORE] \
    [--gap-extend-score GAP_EXTEND_SCORE] \
    [--max-reads-per-cluster MAX_READS_PER_CLUSTER] \
    [--seed SEED] \
    [--orientation-kmer-size ORIENTATION_KMER_SIZE] \
    [--num-threads NUM_THREADS]

Example:

exacto determine-rna-consensus \
    --tsv-file pass2/tumor_pass2_exacto_rna_clusters.tsv \
    --fastq-file pass1/tumor_pass1_exacto_rna_corrected_reads.fastq.gz \
    --output-dir pass2/ \
    --output-prefix tumor_pass2

Description

Determine an RNA consensus sequence for each RNA read cluster.

NoteAt a glance

Inputs: *_exacto_rna_clusters.tsv (the pass-2 cluster-rna-reads run), *.fastq[.gz] (the reads the clusters name — the corrected FASTQ)

Outputs: {prefix}_exacto_rna_consensus.tsv, {prefix}_exacto_rna_consensus.fasta (one consensus per cluster; FASTA records named by cluster ID)

Typical next step: Align the consensus FASTA with minimap2 (--cs is required), then stitch-reference-transcripts

Required arguments

Flag	Type	Description
--tsv-file	str	Input TSV file. Expected columns: ‘cluster_id’, ‘read_name’. This is one of the outputs from exacto cluster-rna-reads.
--fastq-file	str	Input FASTQ file.
--output-dir	str	Output directory.
--output-prefix	str	Output prefix.

Optional arguments

Flag	Type	Default	Description
--match-score	int	0	Match score for partial order alignment, added on a match. abPOA scores in positive magnitudes; a negative value is read as its magnitude.
--mismatch-score	int	4	Mismatch penalty for partial order alignment, a positive magnitude that is subtracted.
--gap-open-score	int	6	Gap-open penalty for partial order alignment, a positive magnitude; a gap of length L costs gap_open + gap_extend * L. Zero selects abPOA’s linear gap model; a negative value is refused.
--gap-extend-score	int	2	Gap-extend penalty for partial order alignment, a positive magnitude charged per gapped base; a value below 1 is refused.
--max-reads-per-cluster	int	1000	Maximum number of reads aligned for one cluster. A cluster of more reads gets its consensus sequence from this many of its reads, drawn at random. 0 aligns all the reads of every cluster.
--seed	int	42	Seed for the reads drawn from a cluster of more than –max-reads-per-cluster reads.
--orientation-kmer-size	int	15	Length of the k-mers by which the reads of a cluster are turned to the orientation of most of them before alignment, at most 32. 0 aligns the reads as they are in the FASTQ file.
--num-threads	int	4	Number of threads.