RNA-seq Analysis — Pipeline Skill (Thin Scaffold)

Overview

Adds decision logic for choosing quantification paths (STAR vs Salmon), strandedness determination, and DESeq2 modeling pitfalls that LLMs routinely get wrong.

Usage

• Activate when choosing between alignment-based (STAR+featureCounts) vs alignment-free (Salmon) quantification
• Activate when setting up DESeq2 from either count source
• Activate when debugging unexpected low counts or weak DE signal

Core Concepts

Decision Logic