> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/miseq.md).

# MiSeq

- [FAQ](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list.md)
- [How to enable email notifications on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000007477.md)
- [Is it possible to perform a primer rehybridization on a MiSeq?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002536.md)
- [MiSeq Flow cell compatibility for v2 and v3 reagent kits](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002538.md)
- [Run setup modes for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000005572.md)
- [Setting up a sample sheet to send all reads to Undetermined in MiSeq Reporter](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000003628.md)
- [What are the MiSeq dimensions and placement requirements?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000007969.md)
- [What are the lab temperature requirements for the MiSeq?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000007967.md)
- [What are the power specifications for the MiSeq?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000007968.md)
- [What color of cap on the MiSeq flow cell container corresponds to which type of flow cell?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000003332.md)
- [What does the MiSeq status bar color mean?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000006205.md)
- [What if I did not name the sample sheet with the MiSeq reagent cartridge barcode number?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002594.md)
- [What is the maximum read lengths and total number of cycles for MiSeq kits?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002595.md)
- [What is the minimum PhiX amount that can be spiked into a run?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002525.md)
- [When do quality scores appear during a sequencing run on the MiSeq?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002600.md)
- [When is the demultiplexing summary generated for analyzed MiSeq runs?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000003372.md)
- [Which Illumina library preparation kits are compatible with the MiSeq?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002521.md)
- [Which controls should be used when sequencing low diversity libraries on a MiSeq?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-faq-list/000002522.md)
- [Troubleshooting](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list.md)
- [How to recover Local Run Manager v3 Account when locked out](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000005751.md)
- [How to troubleshoot MiSeq runs taking longer than usual or expected](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000006023.md)
- [MiSeq RFID Bypass Code生成方法](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000007343.md)
- [MiSeq上开始一个测序反应的时候，遇到Flow Rate检测失败，该如何处理?](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000007115.md)
- [Troubleshooting "@@@ Failed to get temperature" error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001453.md)
- [Troubleshooting "Compensator Move and/or Sensor Failed" errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000008020.md)
- [Troubleshooting "Conflict" errors at end of MiSeq runs](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000008345.md)
- [Troubleshooting "Initialize Cameras before capturing images" error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000007442.md)
- [Troubleshooting "Primary Analysis Not Ready" errors during Pre run Checks on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003755.md)
- [Troubleshooting "TEC2SERVO unrecognize char" error during MiSeq Control Software initialization](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000002865.md)
- [Troubleshooting "Unable to communicate with BaseSpace" error when setting up MiSeq run on Windows 10](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000007849.md)
- [Troubleshooting "Unsuccessfully attempted to launch module type" error with LRMv3 on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003872.md)
- [Troubleshooting "Y home sensor never tripped" error on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000002353.md)
- [Troubleshooting 'Index outside the bounds of the array' error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001432.md)
- [Troubleshooting Cannot get Value value (type Boolean) errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000008532.md)
- [Troubleshooting Cavro Pump Error on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001454.md)
- [Troubleshooting FASTQ Generation failing to start automatically in MiSeq using MiSeq Reporter](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003614.md)
- [Troubleshooting FASTQ generation not occurring automatically after a MiSeq run has completed successfully and successfully uploaded to BaseSpace](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000008692.md)
- [Troubleshooting FPGA RFID ERROR STATUS 2 errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001909.md)
- [Troubleshooting Free Disk Space errors during Pre run Checks on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003753.md)
- [Troubleshooting Invalid Role Errors after Post Run Washes on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000009173.md)
- [Troubleshooting LRM error "Valid index kit must be provided for the selected library prep kit"](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003876.md)
- [Troubleshooting MiSeq "Z Motor The Z stage amp Op amp might not be wired correctly" Error](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001913.md)
- [Troubleshooting MiSeq washes taking extended time to complete](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000002083.md)
- [Troubleshooting MiSeqOverride.cfg Errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003299.md)
- [Troubleshooting Network Connection Active errors during Pre run Checks on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003754.md)
- [Troubleshooting PR2 Bottle Not Detected Error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001451.md)
- [Troubleshooting RFID Not Recognized Error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001459.md)
- [Troubleshooting RFID cannot be written error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001450.md)
- [Troubleshooting Reagent Valve errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001458.md)
- [Troubleshooting Sample Sheet will not Load into MiSeq Control Software](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001455.md)
- [Troubleshooting Sipdown Errors on the MiSeq video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000006824.md)
- [Troubleshooting Stalled Flow Rate Check on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000009288.md)
- [Troubleshooting Waste Bottle is Full notification on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001429.md)
- [Troubleshooting Z Motor Positive soft limit too nonlinear at innermost test point on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000002241.md)
- [Troubleshooting an Object Reference Error on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001428.md)
- [Troubleshooting file is not properly formatted warning on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000009180.md)
- [Troubleshooting frozen MiSeq Control Software](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001890.md)
- [Troubleshooting high cluster density on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000006801.md)
- [Troubleshooting no intensity for index read on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000001461.md)
- [Troubleshooting scratched or damaged flow cells on MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000003192.md)
- [如何在MiSeq系统上重启RTA](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000007341.md)
- [如何排查MiSeq平台上的第一个循环报错的原因？](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-troubleshooting-list/000007340.md)
- [Reference Material](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list.md)
- [How To Power Cycle the MiSeq Video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000005871.md)
- [How to Denature and Dilute Libraries and Spike in PhiX on the MiSeq Video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000007462.md)
- [How to Prepare a MiSeq Sequencing Reagent Cartridge Video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000006670.md)
- [How to Start a Run on the MiSeq Video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000007463.md)
- [How to configure MiSeq Reporter to use a network location as the default output folder](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000002256.md)
- [How to find sample sheet templates for MiSeq Control Software (MCS) v4.0 Local Run Manager](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000003882.md)
- [How to make sure FASTQ generation occurs in MiSeq Reporter when using BaseSpace for analysis](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000003616.md)
- [How to navigate the MiSeq Self Service Resources tool](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000007446.md)
- [How to prepare low concentration (< 2 nM) libraries for sequencing on a MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000006058.md)
- [How to properly format and use a custom reference genome in MiSeq Reporter](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000002212.md)
- [How to set up a PhiX validation run on MiSeq (using software v2.6 and earlier)](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001884.md)
- [How to set up the sample sheet for a PhiX validation run on the MiSeq using IEM](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001244.md)
- [MiSeq Run Quality and Best Practices Support Webinar Video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000008040.md)
- [MiSeq Sequencing Reagents Preparation: Flow cell Video](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000006669.md)
- [MiSeq flow cell tiles by flow cell type](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001672.md)
- [MiSeq output and analysis folder quick reference guide](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000005817.md)
- [MiSeq上机测序时如何准备＜2nM 的文库](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000007417.md)
- [Reference images for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000002700.md)
- [Run folder sizes and Disk Space on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000006711.md)
- [Sample sheet creation for MiSeq Control Software v2.6 and Earlier](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000002396.md)
- [Technical resources for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000007486.md)
- [Thumbnail Image naming conventions for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000003082.md)
- [Upgrading to MiSeq Control Software v4.0](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000005753.md)
- [User supplied consumables for sequencing on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001675.md)
- [Wash Notifications on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001448.md)


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