quantify-rna-abundances

Quantify RNA abundances.

Usage

Template:

exacto quantify-rna-abundances \
    --clusters-tsv-file <clusters_tsv_file> \
    --cluster-reference-matches-tsv-file <cluster_reference_matches_tsv_file> \
    --cluster-splice-junctions-tsv-file <cluster_splice_junctions_tsv_file> \
    --cluster-variants-tsv-file <cluster_variants_tsv_file> \
    --consensus-rna-reference-matches-tsv-file <consensus_rna_reference_matches_tsv_file> \
    --output-dir <output_dir> \
    --output-prefix <output_prefix> \
    [--pseudo-count PSEUDO_COUNT] \
    [--max-iter MAX_ITER] \
    [--tol TOL]

Example:

exacto quantify-rna-abundances \
    --clusters-tsv-file pass2/tumor_pass2_exacto_rna_clusters.tsv \
    --cluster-reference-matches-tsv-file pass2/tumor_pass2_exacto_rna_clusters_reference_transcripts.tsv \
    --cluster-splice-junctions-tsv-file pass2/tumor_pass2_exacto_rna_clusters_splice_junctions.tsv \
    --cluster-variants-tsv-file pass2/tumor_pass2_exacto_rna_clusters_variants_passed.tsv \
    --consensus-rna-reference-matches-tsv-file rna_variants/tumor_exacto_assembled_transcript_reference_transcript_matches.tsv \
    --output-dir abundances/ \
    --output-prefix tumor

Description

Quantify RNA abundances.

At a glance

Inputs: Four pass-2 cluster-rna-reads TSVs (clusters, reference transcripts, splice junctions, variants passed), *_exacto_assembled_transcript_reference_transcript_matches.tsv (from call-rna-transcript-vars)

Outputs: {prefix}_exacto_rna_abundances.tsv (per cluster), {prefix}_exacto_rna_abundances_reference_transcripts.tsv (per reference transcript)

Typical next step: Endpoint — per-cluster and per-reference-transcript abundance estimates

Required arguments

Flag	Type	Description
`--clusters-tsv-file`	`str`	Clusters TSV file. Expected columns: ‘cluster_id’, ‘read_name’. This file is one of the outputs from exacto cluster-rna-reads.
`--cluster-reference-matches-tsv-file`	`str`	Cluster reference matches TSV file. Expected columns: ‘cluster_id’, ‘reference_gene_id’, ‘reference_transcript_id’. This file is one of the outputs from exacto cluster-rna-reads.
`--cluster-splice-junctions-tsv-file`	`str`	Cluster splice junctions TSV file. Expected columns: ‘cluster_id’, ‘chromosome_1’, ‘chromosome_2’, ‘position_1’, ‘position_2’, ‘strand_1’, ‘strand_2’. This file is one of the outputs from exacto cluster-rna-reads.
`--cluster-variants-tsv-file`	`str`	Cluster variants TSV file. Expected columns: ‘cluster_id’, ‘chromosome_1’, ‘position_1’, ‘strand_1’, ‘operation_type_1’, ‘chromosome_2’, ‘position_2’, ‘strand_2’, ‘operation_type_2’, ‘sequence’, ‘variant_type’. This file is one of the outputs from exacto cluster-rna-reads.
`--consensus-rna-reference-matches-tsv-file`	`str`	Consensus RNA reference transcript matches TSV file. Expected columns: ‘assembled_transcript_name’, ‘reference_gene_name’, ‘reference_transcript_id’. This file is one of the outputs from exacto call-rna-transcript-vars.
`--output-dir`	`str`	Output directory.
`--output-prefix`	`str`	Output prefix.

Optional arguments

Flag	Type	Default	Description
`--pseudo-count`	`float`	`0.01`	Pseudo count added to each cluster’s unique read count when the abundances are initialized.
`--max-iter`	`int`	`10000`	Maximum number of expectation-maximization iterations.
`--tol`	`float`	`1e-09`	Convergence tolerance: iteration stops once the largest per-cluster change in relative abundance falls below this.