Bulk RNA-seq Counts QC

Use this skill for bulk RNA-seq read processing, quantification, and count-matrix generation. If the user already has a count matrix and wants contrasts or statistics, use ngs-bulk-rnaseq-differential-expression.

Essential Inputs

Confirm:

• FASTQ or aligned-read inputs and paired-end/single-end status
• organism, genome build, FASTA, GTF, and gene ID convention
• strandedness or permission to infer strandedness
• sample sheet with biological condition, replicate, batch, and library metadata
• desired quantification: gene counts, transcript estimates, or both
• alignment strategy: STAR/Salmon, Salmon-only, featureCounts from BAMs, or existing lab protocol

Route

Prefer nf-core/rnaseq for standard processing when a stable container or HPC runtime is available. Use the local_light Snakemake/Salmon path for small local/devbox feasibility runs when Docker, registry egress, or Nextflow process containers are the blocker.