01_setup_reference.md

Optional setup: small demo reference

Use this guide only if you want to build the small demo reference inside Codespaces.

If you already have a STAR index that you want to use, skip this guide.

Run

bash scripts/codespaces/fetch_public_chr22y_reference.sh
bash scripts/codespaces/build_public_chr22y_index.sh --threads 4

What you get

• .codespaces-demo/data/public_human_chr22y_ref/fasta/genome.fa
• .codespaces-demo/data/public_human_chr22y_ref/genes/genes.gtf
• .codespaces-demo/indices/public_human_chr22y_star

In plain terms

This builds a very small human reference that only contains chr22 and chrY. It is small enough to use in Codespaces and is shared by the single-cell demo guides.

Using your own data

If you want to run real data, this is the place where you would switch from the small demo genome.fa and genes.gtf to your own full reference files and build a new STAR index.

See Using your own data.