Summary
Unlike ribotish predict, the ribotish quality subcommand does not have a -a secondary annotation flag (confirmed by source code inspection of src/run/quality.py). It accepts only a single -g gene annotation file. This issue determines the correct behaviour when --extended_orf_analysis is active and a hybrid GTF (canonical + novel StringTie transcripts) is available.
Background
ribotish quality is a QC/calibration step: it assesses P-site signal quality by measuring reading-frame periodicity against known coding sequences. Its output drives sample-quality decisions, not ORF discovery.
Option A (likely correct) — always pass canonical annotation only
Novel intergenic transcripts (no CDS) contribute zero signal to frame-periodicity metrics and may dilute QC plot readability. This is consistent with the decision made for riboWaltz (canonical-only permanently).
Option B — pass hybrid GTF
Maintains a single GTF path but provides no benefit: CDS-absent transcripts are invisible to frame-periodicity metrics.
Tasks
- Run
ribotish quality with a mixed GTF (CDS-bearing + CDS-absent novel transcripts) and check whether QC metrics change relative to canonical-only input.
- If Option A is confirmed: document that
ribotish quality always uses canonical annotation regardless of --extended_orf_analysis; add an explicit override in conf/modules.config if the pipeline currently passes the wrong GTF.
- Close with findings — likely no module change needed, just pipeline config.
References
Summary
Unlike
ribotish predict, theribotish qualitysubcommand does not have a-asecondary annotation flag (confirmed by source code inspection ofsrc/run/quality.py). It accepts only a single-ggene annotation file. This issue determines the correct behaviour when--extended_orf_analysisis active and a hybrid GTF (canonical + novel StringTie transcripts) is available.Background
ribotish qualityis a QC/calibration step: it assesses P-site signal quality by measuring reading-frame periodicity against known coding sequences. Its output drives sample-quality decisions, not ORF discovery.Option A (likely correct) — always pass canonical annotation only
Novel intergenic transcripts (no CDS) contribute zero signal to frame-periodicity metrics and may dilute QC plot readability. This is consistent with the decision made for riboWaltz (canonical-only permanently).
Option B — pass hybrid GTF
Maintains a single GTF path but provides no benefit: CDS-absent transcripts are invisible to frame-periodicity metrics.
Tasks
ribotish qualitywith a mixed GTF (CDS-bearing + CDS-absent novel transcripts) and check whether QC metrics change relative to canonical-only input.ribotish qualityalways uses canonical annotation regardless of--extended_orf_analysis; add an explicit override inconf/modules.configif the pipeline currently passes the wrong GTF.References
qualitysource: src/run/quality.py (no-aflag)