Bulk RNA-seq

Use this skill as the bulk RNA-seq dispatcher. Route FASTQ/BAM processing to count-generation QC, and route count-matrix statistical analysis to differential-expression guidance.

Essential Inputs

Confirm:

• organism and genome build
• FASTA and GTF, or supported nf-core genome key
• paired-end or single-end reads
• strandedness, or whether to infer strandedness
• sample sheet and metadata
• counts-only vs differential expression
• contrasts, covariates, and batch terms for differential expression

Dispatch