# 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.sh -r -s --analysisFolder ``` The `--analysisFolder` parameter is optional. If no path is provided, output files will be put in a folder under the `/staging/` directory. * WARNING: 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.sh -h ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/dragen-protein-quantification/counting-and-normalization/local-secondary-analysis.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.