# NovaSeq 6000 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/OIe3dy8D8mUKcOT5U0av" alt="" width="563"><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/YwPnjoDsEIEk3rtS7HtG" alt="" width="500"><figcaption></figcaption></figure>

5. Name the run
6. For *Instrument Platform*, select "NovaSeq 6000/6000Dx"
7. For *Secondary Analysis*, select "BaseSpace / Illumina Connected Analytics"
8. Select "Next"
9. For *Application*, the recommendation is to use the default, but the product is compatible with all versions of DRAGEN BCL Convert.

<figure><img src="/files/MgVqymQpiKJlJKgM671m" alt="" width="395"><figcaption></figcaption></figure>

10. For *Library Prep Kit*, select either "Illumina 5-Base DNA Prep" or "Illumina 5-Base DNA Prep with Enrichment"
11. 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/S014kTmT7J6j4zOBfD6L" alt=""><figcaption></figcaption></figure>
12. Select "Next"
13. Leave the following fields as default:
    1. Index Reads
    2. Read Type
    3. Read Lengths
    4. Override Cycles
    5. **WARNING**: Trimming is critical for analysis. Changing these values can result in reduced methylation calling accuracy.

<figure><img src="/files/wYdnFK7uziBVkUk9oEOj" alt="" width="471"><figcaption></figcaption></figure>

14. In the sample table, fill in specific sample information for Sample ID, Well Position, and Project
15. I7 index, Index 1, I5 index, and Index 2 should fill in automatically based on selected Well Position
    1. *Note:* Leave the AdapterRead1 and AdapterRead2 fields blank

<figure><img src="/files/ulCzgv1RiIdMuKO71P9E" alt="" width="497"><figcaption></figcaption></figure>

16. For BarcodeMismatchesIndex1, select "1" (recommended default)
17. For BarcodeMismatchesIndex2, select "1" (recommended default)
18. Select "Next"

<figure><img src="/files/cN6ZZLWOG928BsmOleYV" alt="" width="466"><figcaption></figcaption></figure>

19. Review the Planned Run Details page
20. Select "Export" to export the SampleSheet.csv file


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