# 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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-f308b9111332ea19a9aa90aa700aed781116eb41%2Fimage1.jpg?alt=media\&token=525c69f3-6ed0-4db1-acba-a4317f61ae57)

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-76d176e9e24fcbe59d401fd6aa1030e437c04891%2Fimage2.png?alt=media\&token=534f22d8-072e-4984-ad2e-1f1b04782a1c)

**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 [S](https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000/specifications.html)[pecifications for the NextSeq 1000/2000](https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000/specifications.html).
* If run does not meet yield and Q30 specification and run setup has been ruled out, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for the next steps.

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