Troubleshooting decreased intensity and clusters passing filter at flow cell inlet on NovaSeq 6000

NovaSeq 6000 sequencing runs with low intensity values, and no or low clusters passing filter at the flow cell inlet only are typically caused by fluidics issues during the clustering stages.

If this is observed, collect the following files from the C:\ProgramData\*\Illumina\NovaSeq\NovaSeqTemp<RunID> folder on the instrument:

• RunParameters.xml

• RunInfo.xml

• InterOp folder

• Logs folder

Once collected, contact Illumina Technical Support for further assistance investigating this issue.

\*The ProgramData folder is hidden by default. If this folder is not present, select the View tab in File Explorer and then select the checkbox next to Hidden Items.

For any feedback or questions regarding this article (Illumina Knowledge Article #6690), contact Illumina Technical Support [e-mail].