domains / families / science / splicing-pipeline

splicing-pipeline

separate

Orchestrates the end-to-end bulk short-read alternative-splicing pipeline from FASTQ to differential splicing, chaining fastp QC, cohort-consistent STAR 2-pass alignment (one shared junction DB), junction QC, event-level differential splicing (rMATS-turbo + leafcutter, optional MAJIQ V3), parallel isoform-level DTU (Salmon -> tximport dtuScaledTPM -> DRIMSeq/DEXSeq -> stageR), and sashimi visualization. Use when committing the annotation GTF and a shared 2-pass junction database for the whole cohort, keeping the analysis at splice-aware resolution (never collapsing to gene), choosing event-level vs isoform-level DTU and reconciling them, applying the stageR two-stage gene->transcript FDR, or off-ramping to splice-variant / outlier / long-read / single-cell splicing. Hands mechanism to the alternative-splicing component skills; not a re-teach of any single step.

When to use

• bulk short-read alternative-splicing pipeline
• cohort-consistent STAR 2-pass alignment
• event-level differential splicing
• isoform-level DTU
• reconciling event-level and isoform-level results
• applying stageR two-stage FDR
• sashimi visualization

When not to use

• This pipeline targets **bulk short-read differential splicing between two groups**. For other regimes, use the dedicated skill. | Question | Use instead | |----------|-------------| | "Does this DNA variant alter splicing?" | alternative-s…

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