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add sample data and update getting_started
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VarunAnanth2003 committed Nov 20, 2024
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22 changes: 21 additions & 1 deletion docs/getting_started.md
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Expand Up @@ -163,4 +163,24 @@ If you want to store the output mzTab file in a different location than the curr

This job should complete in < 1 minute.

Congratulations! Casanovo is installed and running.
Congratulations! Casanovo is installed and running in *de novo* mode.

## Try Casanovo-DB on a small example

Now let's use Casanovo to perform database search with the same MGF from above and a FASTA file.
The example MGF file is available at [`sample_data/sample_preprocessed_spectra.mgf`](https://github.com/Noble-Lab/casanovo/blob/main/sample_data/sample_preprocessed_spectra.mgf).
The example FASTA file is available at [`sample_data/human.fasta`](https://github.com/Noble-Lab/casanovo/blob/main/sample_data/human.fasta).

To obtain PSM scores between these spectra and the fasta:
1. Download the example MGF above.
2. Download the example FASTA above.
3. [Install Casanovo](#installation).
4. Ensure your Casanovo conda environment is activated by typing `conda activate casanovo_env`. (If you named your environment differently, type in that name instead.)
5. Perform database search with Casanovo-DB, replacing `[PATH_TO_MGF]` with the path to the example MGF file that you downloaded AND replacing `[PATH_TO_FASTA]` with the path to the example FASTA file that you downloaded:
```sh
casanovo db-search [PATH_TO_MGF]/sample_preprocessed_spectra.mgf [PATH_TO_FASTA]/human.fasta
```

This job should complete in < 15 minutes.

Congratulations! Casanovo is installed and running in db-search mode.
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