RNA-Seq Alignment with STAR (Using Docker)

This repository demonstrates a minimal working example of aligning RNA-Seq reads to a toy genome using STAR inside a Docker container.

Project Structure

• Dockerfile: Installs STAR and dependencies
• scripts/run_star.sh: Runs genome generation and alignment
• data/: Toy genome, GTF, and FASTQ files
• output/: Alignment results (not tracked by Git)

How to Use

docker build -t star-docker .

Run the STAR alignment

docker run --rm
-v $(pwd)/output:/app/output
-v $(pwd)/data:/app/data
-v $(pwd)/scripts:/app/scripts
star-docker bash scripts/run_star.sh

Example Data

• toy_genome.fa: A tiny artificial reference genome
• toy_genes.gtf: A GTF annotation file with a single exon
• sample.fastq: A single-end FASTQ file with 1 read

Output Files

After running the pipeline, the output/ directory will contain:

• Aligned.sortedByCoord.out.bam: Final aligned BAM file
• Log.out: STAR alignment log
• SJ.out.tab: Splice junction output (empty for toy example)

Notes

• The FASTQ file must have equal-length sequence and quality lines
• The GTF file must contain exon features with coordinates that match the FASTA reference
• STAR is compiled and run inside the container using Ubuntu 20.04

License

MIT License. Use and modify freely.