# How to Troubleshoot Clustering Failures on the MiSeq i100 Series

**Background**

The MiSeq i100 uses clusters of clonally replicated template strands to generate the light signal required for identifying the appropriate base call at each cycle. Issues with the instrument, consumables, or library quality cause the clustering process to fail, resulting in sequencing runs with low intensity, quality scores, and clusters passing filter.

*Reduced Intensities*

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-a11b3a1ee2bb27f50f4bc55cdf2959e6da585d71%2Fimage1.png?alt=media)

*Reduced Quality Scores*

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-a5d2919ad79b5fdc41dbeb28a81535c66369e387%2Fimage2.png?alt=media)

*Reduced Passing Filter (%PF)*

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-73b678d9c574eb003ecc02280228e36eea33da6f%2Fimage3.png?alt=media)

See the following steps to investigate and resolve these issues.

**Troubleshooting Actions**

1. Run the instrument System Health Checks on the MiSeq i100 instrument.
   1. See [How to Setup the System Health Checks on the MiSeq i100 Series Instruments](https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009206) for additional details.
2. Review library quality and quantification.
   1. See [Library quantification and quality control quick reference guide](https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000001247) for additional details.
3. If System Health Checks are passing and no issues identified with library quality or quantification, repeat sequencing run using new consumables.

For additional assistance with troubleshooting clustering failures on the MiSeq i100 Series, contact Illumina [Tech Support](https://www.illumina.com/company/contact-us.html).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9347), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009347%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |