alterlab-rnaseq-quant

name	alterlab-rnaseq-quant
description	Quantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --validateMappings --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2. Warns that salmon's index format changed to SSHash (rebuild pre-v1.11.2 indices) and that 'salmon alevin' was REMOVED (single-cell now uses piscem + alevin-fry). Use when quantifying RNA-seq transcript abundance, running salmon or kallisto, building a decoy-aware index, or wiring tximport to DESeq2; for differential expression use alterlab-pydeseq2, for FASTQ-to-VCF variant calling use alterlab-nf-core-sarek. Part of the AlterLab Academic Skills suite.
license	MIT
allowed-tools	Read Write Edit Bash(python:*) Bash(uv:*) Bash(salmon:*) Bash(kallisto:*) Bash(kb:*)
compatibility	Requires the salmon and/or kallisto CLI on PATH (conda/bioconda or a container). salmon v1.11.4 and kallisto v0.52.0 are the versions this skill targets; the tximport/tx2gene helper runs under `uv run python` with pure stdlib (no pandas needed). No API key or account required; all work is local.
metadata	{"skill-author":"AlterLab","version":"1.0.0","last_updated":"2026-06-06","depends_on":"alterlab-pydeseq2 (downstream differential expression)"}

RNA-seq Quantification — salmon & kallisto Transcript Abundance

The command-line quantification entry point for bulk RNA-seq: take raw FASTQ reads plus a reference transcriptome and produce transcript-level abundance estimates (counts + TPM) with salmon (selective alignment) or kallisto (pseudoalignment via kb-python), then aggregate to the gene level with tximport/tximeta and hand off to alterlab-pydeseq2 for differential expression. It is the raw-data-to-count-matrix pipeline that the repo's Python analysis skills assume already ran.

Quick Start

Quantify these RNA-seq FASTQs with salmon and a decoy-aware index
Build a salmon gentrome index from this transcriptome + genome
Run kallisto / kb count on my paired-end reads
Turn my salmon quant.sf files into a gene-level count matrix for DESeq2

→ Build a decoy-aware index once, run salmon quant (or kb count) per sample, then run scripts/build_tx2gene.py + scripts/import_quant.py to make the tximport gene matrix and route it to alterlab-pydeseq2.

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When to Use This Skill

Use this skill when the request is about getting from FASTQ to transcript or gene abundance with a lightweight quantifier:

• "Quantify my RNA-seq with salmon / kallisto."
• "Build a decoy-aware salmon index (gentrome + decoys.txt)."
• "Run selective alignment with --validateMappings --gcBias."
• "I have quant.sf files — make me a gene-level count matrix for DESeq2."
• "Set up tximport / tximeta with a tx2gene map."
• "Use kb-python / kb count to pseudoalign these reads."

Does NOT Trigger — route these to the right sibling

The request is really about…	Route to
Differential expression on a count matrix (DESeq2 Wald tests, FDR, volcano)	alterlab-pydeseq2
Single-cell RNA-seq quantification (was salmon alevin)	piscem + alevin-fry — see references/single_cell_alevin.md; downstream → /