Process RNA-seq from reads to enrichment
bulk-rnaseqskillsetup L3★27,559
K-Dense-AI/scientific-agent-skills ↗What it does
Route tasks to specialist skills
Best for
When analyzing bulk RNA-seq from raw reads through differential expression and pathway enrichment with reproducible, quality-gated pipelines.
Inputs
- · FASTQ files
- · Sample metadata
- · Reference genome/annotation
Outputs
- · Gene-level counts matrix
- · QC reports
- · Differential expression table
Requires
- · STAR
- · FastQC
- · Salmon
Preconditions
- · FASTQ files on disk
- · Reference genome + annotation available
- · FastQC/STAR/Salmon installed or Nextflow + Docker
Failure modes
- · Strandedness mismatch yields reverse-complement counts
- · Reference genome version mismatch causes poor alignment
- · Adapter content not trimmed inflates downstream counts
Trust signals
- · Routes through nf-core/rnaseq (peer-reviewed)