> 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/illumina-trupath-genome/sequencing-run-setup/novaseq-x-run-planning-bcl-convert.md).

# 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/Sj1OvTATorfNs9pFqInp" 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 <a href="#specify-run-settings" id="specify-run-settings"></a>

<figure><img src="/files/9W37pRHLGafeMHIPkHhK" alt=""><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: 0
   3. Index 2: 0
   4. Read 2: 151
9. Select "Next"
10. For *Application*, select "DRAGEN BCL Convert - 4.4.10"

<figure><img src="/files/i5x4KN9CPuGdhND78dk0" alt=""><figcaption></figcaption></figure>

11. For *Library Prep Kit*, select either "Illumina TruPath Genome (C2)" or "Illumina TruPath Genome (C8)"
12. For *Index Adapter Kit*, select "Not Applicable"

    <figure><img src="/files/zYRcwp0JJo63h5N4ouDh" 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
15. In the sample table, fill in specific sample information for Sample ID and Project.\
    Note that ***Sample ID's must be unique*****.**

{% hint style="info" %}
Illumina TruPath Genome flow cells support one sample per lane. For the C2 flow cell, enter samples information up to two samples. For the C8 flow cell, enter information for up to eight samples.
{% endhint %}

<figure><img src="/files/uZBEyjLqHXoF2Gu4Q2HP" alt=""><figcaption></figcaption></figure>

16. For analysis settings, select "**No**" for Combine sample FASTQs across lanes.<br>

    <figure><img src="/files/w0rty0qVpc18KAQSlkC2" alt=""><figcaption></figcaption></figure>
17. For auto-detect demux mode, select "**None**"

<figure><img src="/files/Xzf0CrLYbudah9OiHVME" alt=""><figcaption></figcaption></figure>

16. For auto-detect minimum number select "**Auto (default)**"

<figure><img src="/files/lm2HRqXDDXtoOxzECEjK" alt=""><figcaption></figcaption></figure>

17. Review the **Planned Run Details Page:**<br>

    <figure><img src="/files/qcKmVgoc3oimvX9P5z6Q" alt=""><figcaption></figcaption></figure>
18. Add another configuration if desired.
19. Select **"Export"** to export the SampleSheet.csv file. **Attach the Sample Sheet to the Sequencing Run during the run setup workflow for performing a manual run on the NovaSeq X**. The Sample Sheet will be copied to the sequencing run output folder, where it may be used for DRAGEN BCL Convert via on-prem server.


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