starGen

starGen is a command-line RNA-seq pipeline focused on STAR alignment, QC visualization, and featureCounts quantification — optimized for SLURM clusters and scalable workflows.

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Features

• Generate SLURM batch scripts for STAR alignment
• Automated per-sample STAR QC summary extraction and visualization (interactive plots & static PNGs)
• FeatureCounts gene quantification on aligned BAMs
• Project scaffolding with starGen init for easy setup
• Flexible config-driven workflow, customizable with CLI flags
• Designed for HPC clusters with SLURM support

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Installation

Install starGen into a conda environment using > python 3.10

pip install git+https://github.com/BioinformaticsMUSC/starGen.git

Usage

# Initialize a new project folder
starGen init my_rnaseq_project

cd my_rnaseq_project

# Modify the config.cfg file (see below)

# Generate SLURM scripts for STAR alignment
starGen generate --config config.cfg

# Load modules if necessary

module load biocontainers
module load star/2.7.10a

# Submit jobs (via SLURM)
bash submit_all.sh

# Visualize STAR QC metrics after alignments
starGen qc

# Run featureCounts quantification on BAM files
module load biocontainers
module load subread
starGen featurecounts --gtf-file /path/to/annotation.gtf

Configuration

Your config.cfg file should be updated with the following information:

BASE_DIR=./fastqs
STAR_INDEX=/path/to/star/index
GTF_FILE=/path/to/annotation.gtf