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About bulk-rnaseq
bulk-rnaseq
Prepares bulk RNA-seq FASTQ, Salmon
bulk-rnaseq is an agent skill that prepares bulk RNA-seq reads and quantification output for a reproducible gene-level comparison. It takes FASTQ files, along with Salmon, STAR or featureCounts output, and gets them ready for differential expression. It owns sample validation, the recipes that turn reads into counts, and the handoff of counts and metadata to later steps. Statistical fitting and enrichment analysis are left to specialist skills. The skill defines defensible work as three things: reproducible, with pinned tool versions, containers where possible, recorded parameters and fixed random seeds; quality-gated, with QC inspected and acted on before, during and after quantification; and statistically sound, with adequate replication, a design that matches the biology, correct handling of counts, and FDR-controlled testing. The pipeline it describes runs FastQC and trimming, then alignment and quantification with STAR or Salmon, then counts, then differential expression with pydeseq2, then enrichment, then figures. It covers nf-core/rnaseq as well as standalone quantification. Use it when you are setting up a bulk RNA-seq comparison.
- Price
- Free
- Made by
- k-dense-ai
- Category
- AI Skills
- Website
- github.com/k-dense-ai/scientific-agent-skills/bulk-rnaseq