bulk-rnaseq
Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2. For single-cell data use scanpy; for statistical fitting alone use pydeseq2.
- Version
- 2.0
- License
- MIT
- Compatibility
- Requires Python 3.11+ with pandas and numpy; Salmon import also needs pytximport. Read processing needs Nextflow with containers or standalone bioinformatics tools. Network access is needed for installation and reference downloads.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/bulk-rnaseq/SKILL.md
- skills/bulk-rnaseq/SKILL_CN.md
- skills/bulk-rnaseq/references/counts-and-handoff.md
- skills/bulk-rnaseq/references/design-and-qc.md
- skills/bulk-rnaseq/references/upstream-manual.md
- skills/bulk-rnaseq/references/upstream-nfcore.md
- skills/bulk-rnaseq/scripts/_tabular.py
- skills/bulk-rnaseq/scripts/build_counts_matrix.py
- skills/bulk-rnaseq/scripts/validate_samplesheet.py
Every link opens the file at its source, pinned to the revision this page describes.