Troubleshooting NextSeq 1000/2000 low read 1 intensity

NextSeq 1000/2000 run with low intensities on Read 1 and Index 1 which then recovers for Index 2 and Read 2 are typically caused by issues with poor priming Read 1 and Index 1.

Issues with priming can be caused by the following root causes:

• Library design or custom primers.

• Custom primer not proper loaded into the reagent cartridge when needed.

• Reagent cartridge consumable quality.

Diagnosing

The Intensity Data by Cycle charts will show drops at the start of Read 1 and/or Index 1.

Troubleshooting steps:

• Review library design, custom primers and where custom primer loaded, if applicable.

• If run meets yield and Q30 specification, proceed with downstream analysis of the run.

  • See Specifications for the NextSeq 1000/2000.

• If run does not meet yield and Q30 specification and run setup has been ruled out, contact Illumina Technical Support for the next steps.

For any feedback or questions regarding this article (Illumina Knowledge Article #7095), contact Illumina Technical Support [e-mail].