domains / families / science / rnaseq-to-de

rnaseq-to-de

separate

Orchestrates the end-to-end bulk RNA-seq differential-expression pipeline from FASTQ to an annotated DE gene table, chaining fastp QC/trim, Salmon (decoy-aware) or STAR+featureCounts quantification, tximport gene-level collapse, DESeq2/edgeR/limma-voom testing, apeglm shrinkage, and VST-based visualization. Use when committing the reference release and gene-ID namespace once for the whole run, sequencing steps in the defensible order (tximport before DE, raw counts into the model, VST only for viz/clustering), choosing alignment-free vs align-then-count and the DE engine, setting strandedness correctly, keeping batch in the design instead of correcting-then-testing, or handing the signed ranking statistic to downstream enrichment. Hands mechanism to the component skills; not a re-teach of any single step.

When to use

• bulk RNA-seq differential expression
• FASTQ to annotated DE gene table
• chaining fastp QC/trim
• Salmon or STAR+featureCounts quantification
• tximport gene-level collapse
• DESeq2/edgeR/limma-voom testing
• apeglm shrinkage
• VST-based visualization

When not to use

• re-teaching any single step
• teaching component skill mechanisms

Skill page

Source