> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/local-secondary-analysis.md).

# Local Secondary Analysis

DRAGEN Protein Quantification can be run locally after the installation of the local solution on a DRAGEN phase 4 server by an FAS.

To initiate a run:

```
run_DRAGEN_Protein_Quantification_v<version>.sh
    -r <full path to run folder>
    -s <full path to sample sheet>
    --analysisFolder <full path to output folder> 
```

The `--analysisFolder` parameter is optional. If no path is provided, output files will be put in a folder under the `/staging/` directory.

* <mark style="color:$warning;">WARNING</mark>: Currently, using a path off the DRAGEN server as an `--analysisFolder` (for example, to network attached storage) may cause an analysis failure. It's recommended to output the results to the DRAGEN server itself.

The `-s` parameter is optional if the sample sheet file is included in the run folder.

For details on the parameters used with the script, execute the following command.

```
run_DRAGEN_Protein_Quantification_v<version>.sh -h
```


---

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