# NovaSeq X Run Planning - BCL Convert

### Log in to BaseSpace (BSSH) <a href="#pre-sequencing" id="pre-sequencing"></a>

Navigate to either the BSSH private domain or Illumina's public BSSH domain. Sign in with the appropriate credentials.

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-f5c6e39d1c3100988b3388a907a954e9e4e15e79%2Fimage%20(6)%20(2).png?alt=media" alt=""><figcaption></figcaption></figure>

1. Access the appropriate workgroup to plan the sequencing run
2. Select "Runs" from the top panel
3. Select "New Run"
4. Select "Run Planning" from the right-hand dropdown

### Specify Run Settings

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5. Name the run
6. For *Instrument Platform*, select "NovaSeq X Series"
7. For *Secondary Analysis*, select "BaseSpace / Illumina Connected Analytics"
8. For Read Lengths:
   1. Read 1: 151
   2. Index 1: 10
   3. Index 2: 10
   4. Read 2: 151
9. Select "Next"
10. For *Application*, the recommendation is to use the latest version, but the product is compatible with all versions of DRAGEN BCL Convert.

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-f60a7bdc082313f7dfdecff87934680d09cc20e2%2Fimage%20(1)%20(1)%20(2)%20(1)%20(1).png?alt=media" alt="" width="563"><figcaption></figcaption></figure>

11. For *Library Prep Kit*, select either "Illumina 5-Base DNA Prep" or "Illumina 5-Base DNA Prep with Enrichment"
12. For *Index Adapter Kit*, select the appropriate kit from the available options ("Illumina DNA-RNA UD Indexes, Set **X** Tagmentation" where **X** is the appropriate plate version; if pooling indexes from multiple plates, select "A B C D" version)<br>

    <figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-aed3a2f5039a0baa14a6f7e5a89a358b481300ec%2Fimage%20(130).png?alt=media" alt=""><figcaption></figcaption></figure>
13. Select "Next"
14. Leave the following fields as default:
    1. Adapter Read 1
    2. Adapter Read 2
    3. Override Cycles
    4. **WARNING**: Trimming is critical for analysis. Changing these values can result in reduced methylation calling accuracy.

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-4d47dadfadd8706a7d8e46017e64f0be18ce1f97%2Fimage%20(2)%20(1)%20(2)%20(1).png?alt=media" alt="" width="563"><figcaption></figcaption></figure>

15. In the sample table, fill in specific sample information for Sample ID, Well Position, and Project
    1. I7 index, Index 1, I5 index, and Index 2 should fill in automatically based on selected Well Position
    2. *Note*: Leave *Barcode Mismatches Index 1* and *Barcode Mismatches Index 2* as their default values

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-7e52458e061ced19ca8691b4f5b4eea2be9baaaf%2FScreenshot%202025-04-23%20184159.png?alt=media" alt="" width="563"><figcaption></figcaption></figure>

16. Select "Next"
17. Review the Planned Run Details page

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-ef4f3c6c360feaa05a9cf95e7d22853114e32f7f%2FScreenshot%202025-04-23%20184353.png?alt=media" alt="" width="470"><figcaption></figcaption></figure>

18. Add another configuration if desired
19. Select one of the following options:
    1. Select "Export" to export the SampleSheet.csv file
    2. Select "Save as Planned" to save the planned run