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Bulk RNA Sequencing

Domain key: rnaseq

Bulk RNA-seq measures gene expression across a population of cells. Codaris builds nf-core-compliant DSL2 pipelines covering QC → trimming → alignment → quantification → QC aggregation.

Step Tool Notes
QC FastQC Per-read quality metrics
Trimming TrimGalore Adapter + quality trimming
Alignment STAR Splice-aware, gold standard for DGE
Quantification Salmon Pseudo-alignment for transcript counts
Feature counting featureCounts (Subread) Gene-level counts for DGE
QC aggregation MultiQC Aggregates all QC logs

Best Practices Enforced

  • TrimGalore is run before any alignment — raw reads are never aligned directly
  • STAR is used for differential gene expression workflows; Salmon for transcript-level analysis
  • MultiQC is always the final step, aggregating FastQC, STAR, featureCounts, and Salmon logs
  • Genome and GTF references must be supplied explicitly — Codaris will not hardcode paths

Example Prompts

Build a bulk RNA-seq pipeline for human paired-end reads,
aligned to GRCh38, with featureCounts for DGE analysis

Create an RNA-seq pipeline using Salmon for transcript quantification —
I don't need genome alignment, just quasi-mapping

codaris > Review my RNA-seq pipeline and check if STAR index parameters
          are appropriate for 150bp paired-end reads

Pipeline Skeleton

A Codaris-generated RNA-seq pipeline follows this structure:

mypipeline/
├── main.nf
├── nextflow.config
├── conf/
│   ├── base.config
│   └── modules.config
├── workflows/
│   └── mypipeline.nf
├── subworkflows/local/
│   ├── align_star/main.nf
│   └── quantify_salmon/main.nf
└── modules/nf-core/
    ├── fastqc/
    ├── trimgalore/
    ├── star/align/
    ├── salmon/quant/
    └── multiqc/