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Flex (work in progress)

This guide is not finished yet.

You can still use it to see the current command shape and file layout.

Preview the current version

bash scripts/codespaces/run_flex_public_demo.sh --dry-run

Run the current version

bash scripts/codespaces/run_flex_public_demo.sh

What works now

  • small demo reference setup
  • small shared single-cell input
  • Flex config and wrapper wiring

What is still missing

  • a stronger public Flex demo dataset
  • a cleaner end-to-end demo result

Using your own data

For a real Flex run, you will usually need your own FASTQs, whitelist, barcode settings, probe set, and a new filtered reference and STAR index.

See Using your own data.