# 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="/files/rIhd45y0oUBIl7eWhhPq" 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

<figure><img src="/files/GsXeAJ7VsSSpKmQQIdZ7" alt="" width="485"><figcaption></figcaption></figure>

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="/files/5p0gfEC5lwFuEiEx1sG8" 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="/files/bfPdTx9xOBJb6ekIGZbC" 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="/files/25jvYEiqtVijSXuofSUd" 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="/files/sZZxQ5deX1oc7LNtDOlt" alt="" width="563"><figcaption></figcaption></figure>

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

<figure><img src="/files/uYiNXX8hnYxr4bbXfcU6" 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


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