bio-splicing-pipeline - RNA-seq Alternative Splicing Analysis Pipeline
End-to-end alternative splicing analysis from FASTQ to differential splicing results
Tags
Updated: 2026-03-25Capabilities
Typical Inputs
What this skill does
- Trim FASTQ reads
- Align RNA-seq reads
- Perform junction QC
- Run differential splicing analysis
- Filter significant events
- Generate sashimi plots
- Analyze isoform switching
Inputs
- FASTQ files
- STAR genome index
- Annotation GTF file
- Sample condition lists
- Reference BED file
Outputs
- Aligned BAM files
- Differential splicing results
- Sashimi plot PDFs
- QC reports
- Filtered event tables
Requirements
- STAR 2.7.11+
- fastp 0.23+
- rMATS-turbo
- numpy 1.26+
- pandas 2.2+
- ggsashimi
- Optional: IsoformSwitchAnalyzeR