| name | bulkrna-splicing |
| description | Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events. Skip if you only have count-level DE (use bulkrna-de) or for splicing in single-cell or spatial data (currently unsupported). |
| version | 0.3.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["bulkrna","splicing","alternative-splicing","PSI","rMATS","SUPPA2"] |
bulkrna-splicing
When to use
Run AFTER rMATS or SUPPA2 has produced its splicing-event table — this
skill consumes that output (not raw alignments). Computes per-event
ΔPSI (delta percent-spliced-in), flags events crossing significance and
ΔPSI thresholds, and groups results by event type (SE / A3SS / A5SS /
MXE / RI).
Inputs & Outputs
| Input | Format | Required |
|---|
| Splicing event table | .csv from rMATS or SUPPA2 (event_id, type, ΔPSI, p-value cols) | yes (or --demo) |
--dpsi-cutoff | float | default 0.1 (events with abs ΔPSI ≥ this) |
--padj-cutoff | float | default 0.05 (significance threshold) |
| Output | Path | Notes |
|---|
| All events | tables/splicing_events.csv | full annotated event table |
| Significant events | tables/significant_events.csv | filtered by --dpsi-cutoff and --padj-cutoff |
| ΔPSI distribution | figures/dpsi_distribution.png | histogram with cutoff lines |
| Event-type breakdown | figures/event_type_distribution.png | SE / A3SS / A5SS / MXE / RI counts |
| Volcano | figures/volcano_splicing.png | ΔPSI vs -log10(padj) |
| Report | report.md + result.json | always |
Flow
- Load splicing event table. Hard-fail at
bulkrna_splicing.py:365,368 on missing or invalid --input.
- Validate the fixed input schema: must contain columns
event_type, gene, delta_psi, padj (bulkrna_splicing.py:153-155). No format detection — caller must pre-flatten rMATS / SUPPA2 output to this schema.
- Filter by
--dpsi-cutoff AND --padj-cutoff.
- Group by event type; render distribution + volcano + bar plots.
- Emit
tables/splicing_events.csv (full) + tables/significant_events.csv (filtered) + report.
Gotchas
- This skill consumes the SPLICING TABLE, not BAM or FASTQ. Run rMATS or SUPPA2 upstream and feed their output here. The wrapper does not perform splicing detection itself — feeding it BAM files raises a parser error or silently produces an empty result.
--dpsi-cutoff is the ABSOLUTE value of ΔPSI. Default 0.1 keeps events with |ΔPSI| ≥ 0.1, including both inclusion-up and inclusion-down. Set to 0 to keep all directionally significant events.- Input schema is fixed:
event_type, gene, delta_psi, padj (with optional pvalue and event_id). The script does NOT auto-detect rMATS vs SUPPA2 column conventions — if your input uses rMATS's IncLevelDifference/FDR or SUPPA2's dPSI/pval natively, rename columns first or the loader will silently drop your data.
- Event-type breakdown depends on the upstream tool's classification. rMATS reports SE / A3SS / A5SS / MXE / RI as separate files; SUPPA2 uses an EVENT field. Concatenate / re-label these into a single
event_type column before feeding the skill, or the breakdown bar chart under-counts.
Key CLI
python omicsclaw.py run bulkrna-splicing --demo
python omicsclaw.py run bulkrna-splicing \
--input rmats_se.csv --output results/
python omicsclaw.py run bulkrna-splicing \
--input suppa2_events.csv --output results/ \
--dpsi-cutoff 0.2 --padj-cutoff 0.01
See also
references/parameters.md — every CLI flag and tuning hintreferences/methodology.md — rMATS vs SUPPA2 format conventions, event-type taxonomyreferences/output_contract.md — exact output directory layout- Adjacent skills:
bulkrna-de (parallel: gene-level DE, complements exon-level splicing), bulkrna-enrichment (downstream: pathway view of splicing-affected genes via gene-symbol mapping)
