NextSeq 1000/2000 Run Planning - BCL Convert

This page gives an overview of how to plan a sequencing run on BaseSpace for the NextSeq 1000/2000.

Log in to BaseSpace (BSSH)

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

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

1. Name the run

2. For Instrument Platform, select "NextSeq 1000/2000"

3. For Secondary Analysis, select "BaseSpace / Illumina Connected Analytics"

4. Select "Next"

5. For Application, the recommendation is to use the default, but the product is compatible with all versions of DRAGEN BCL Convert.

6. For Library Prep Kit, select either "Illumina 5-Base DNA Prep" or "Illumina 5-Base DNA Prep with Enrichment"

7. 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)

   
8. Select "Next"

9. 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.

      
10. In the sample table, fill in specific sample information for Sample ID, Well Position, and Project

11. 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

12. For BarcodeMismatchesIndex1, select "1" (recommended default)

13. For BarcodeMismatchesIndex2, select "1" (recommended default)

    
14. Select "Next"

    
15. Review the Planned Run Details page

16. Select "Export" to export the SampleSheet.csv file