This repository contains a publication-ready RNA-seq quantification pipeline built around Salmon for lightweight and accurate transcript quantification.
It automates the full workflow from SRA download ? FASTQ generation ? Transcript quantification (Salmon), followed by R-based downstream analysis (DESeq2, functional enrichment, and visualization). The pipeline is designed for reproducibility, modularity, and high-performance computing environments, with detailed timing logs for benchmarking.
- Fully automated and parallelized
- Ready for downstream DESeq2 analysis in R
- Conda-based reproducible environment via
environment.yml - Organized directory structure for clarity and reproducibility
mkdir -p ~/references/hg38 cd ~/references/hg38
conda env create -f environment.yml
conda activate salmon-rnaseq