from awesome-bio-agent-skills25
End-to-end pipeline for short-read bulk RNA-seq alternative splicing analysis: QC, STAR 2-pass alignment, junction QC, rMATS differential splicing, isoform swit
Provides a complete workflow to analyze alternative splicing from raw FASTQ to differential splicing results in bulk short-read RNA-seq experiments. The skill documents steps for QC (fastp), STAR 2-pass alignment, junction quality control, differential splicing with rMATS-turbo, optional isoform-switching analyses (IsoformSwitchAnalyzeR), and sashimi plot generation for visualization.
Use when you have cohort-style short-read RNA-seq data and need to detect differential splicing between two groups, perform QC on junction detection, or generate publication-ready visualizations of splicing events. Not suitable for single-sample rare-disease outlier detection, splice-variant prediction workflows, or long-read full-isoform analysis.
Agents that can orchestrate long-running bioinformatics workflows or output shell commands and scripts (e.g., agents with shell/cluster submission support, or that can generate reproducible pipelines).
This skill has not been reviewed by our automated audit pipeline yet.
