> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/basespace/sequence/plan-runs/multi-analysis-planned-run/reference-files.md).

# NovaSeq X Series Custom Reference File

To perform a secondary analysis, an Application may require certain types of files, such as:

* AuxCnvPanelOfNormalsFile - for Enrichment workflow
* AuxNoiseBaselineFile - for Enrichment workflow
* BedFile - for Enrichment workflow
* RnaGeneAnnotationFile - for RNA workflow

Reference files for NovaSeq X analysis are managed from **Resources** page.

* Select **Resources** from the user menu on the top right of Sequence Hub page
* Select **Reference Files** tab to see the list of reference files available for use in the run planning.
* Both standard and custom files are included in the list.

**Import a Custom Reference File**

1. Select Import Custom Reference File to upload a custom file.
2. After file upload is completed,
   * Select the correct File Type. Run Planning tool will associate the new custom file with the Application based on the selected File Type.
   * Select one or more reference genome(s) that should be associated with the file.
   * **\[Optional]** Enter a description for the custom reference file.
3. Select Save.

**Edit a Custom Reference File**

To edit a custom reference file's metadata, go to the listing page and select the file. Update the information on the Edit page and save it upon completion.

To update the file content, select Import Custom Reference File from the listing page and upload the new file.

**Delete a Custom Reference File**

To delete a custom reference file, go to the listing page, and select the delete icon beside the file.


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