02_bulk.md

Bulk

This is the easiest full demo.

The demo uses a small public bulk RNA-seq subset with 25000 read pairs.

What you need

• a STAR index
• if you do not have one, you can use your own or start with the small setup guide

Preview first

bash scripts/codespaces/run_bulk_public_demo.sh \
  --dry-run \
  --genome-dir /path/to/star_bulk_index

Run it

bash scripts/codespaces/run_bulk_public_demo.sh \
  --run \
  --genome-dir /path/to/star_bulk_index

What you get

• .codespaces-demo/runs/bulk_public_demo/RUN_COMMAND.sh
• .codespaces-demo/runs/bulk_public_demo/Aligned.sortedByCoord.out.bam
• .codespaces-demo/runs/bulk_public_demo/ReadsPerGene.out.tab

These are output files, not shell commands.

Verify outputs

Run the verifier:

bash scripts/codespaces/verify_bulk_public_demo_outputs.sh \
  --outdir .codespaces-demo/runs/bulk_public_demo

If you want to inspect the files manually:

ls -lh \
  .codespaces-demo/runs/bulk_public_demo/Aligned.sortedByCoord.out.bam \
  .codespaces-demo/runs/bulk_public_demo/ReadsPerGene.out.tab

head -n 8 .codespaces-demo/runs/bulk_public_demo/ReadsPerGene.out.tab

If you only prepared a dry run, execute the saved command script with:

bash .codespaces-demo/runs/bulk_public_demo/RUN_COMMAND.sh

If you already know STAR

This guide mostly saves time by downloading a small public dataset and writing the full command for you.

Using your own data

For a real bulk dataset, replace the demo FASTQs with your own files and point --genome-dir to the STAR index built from the reference you want to use.

See Using your own data.