> 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-ruo.md). # MiSeq RUO - [Reference Material](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list.md) - [Best practices for maintaining the computer on a MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000006708.md) - [Chemistry and imaging on MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000003757.md) - [Consumable Part Numbers for the MiSeq and Total SBS cycles available](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000005842.md) - [Custom sequencing primers on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000002414.md) - [Enabling run storage and analysis in BaseSpace for MiSeq runs](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000003618.md) - [File paths for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001678.md) - [Frequently asked questions about upgrading to MiSeq Control Software v4.0](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000005752.md) - [How to Power Cycle the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001894.md) - [How to check network settings on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000002383.md) - [How to clean the MiSeq flow cell holder](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000003500.md) - [How to generate RFID bypass codes for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001528.md) - [How to generate an RFID bypass code in MyIllumina Video](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000005859.md) - [How to stop and restart RTA on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000002031.md) - [Recommendations for optimal cluster density and PhiX loading concentrations on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001676.md) - [Specifications for the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001670.md) - [Troubleshooting](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list.md) - [Best practices to avoid low cluster density on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001844.md) - [How to Check if a MiSeq Reagent Cartridge was pierced during a run](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000003497.md) - [How to access Windows on the MiSeq if there is black screen at boot up](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001658.md) - [How to troubleshoot The process cannot access the file error on MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001910.md) - [Troubleshooting "Access to the path 'Global\Local Run Manager' is denied" on MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000008538.md) - [Troubleshooting "Camera exception, error= 360: Failed to perform sBCa" error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000007301.md) - [Troubleshooting FPGA Timeout Errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001444.md) - [Troubleshooting MiSeq Control Software (MCS) v4 stalling during initialization](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000005502.md) - [Troubleshooting Y Motor Errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001452.md) - [Troubleshooting Z motor errors occurring mid run on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001850.md) - [Troubleshooting a Focus Mirror Error on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001449.md) - [Troubleshooting a MiSeq "Consecutive Camera Failure Limit has been Exceeded for this Run" error](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000005566.md) - [Troubleshooting a bubble in MiSeq flow cell](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001996.md) - [Troubleshooting best focus errors occurring mid run on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001849.md) - [Troubleshooting cycle 1 errors on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001430.md) - [Troubleshooting failed MiSeq system checks](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000007050.md) - [Troubleshooting low cluster density on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001445.md) - [Troubleshooting mid run shutdowns or reboots on the MiSeq](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000002092.md) - [FAQ](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list.md) - [Can MiSeq Reagents be stored at 80°C rather than 20°C?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000008114.md) - [Can Sequencing Analysis Viewer (SAV) be used with the MiSeq System to view primary analysis results?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002601.md) - [Can a MiSeq post run wash be performed every week instead of entering standby mode?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000006976.md) - [Can a MiSeq v2 flow cell be used for sequencing with a MiSeq v3 reagent cartridge?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002317.md) - [Can an entire index be N padded in Miseq Reporter?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000003624.md) - [Can an expired reagent cartridge be used for a MiSeq run?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002254.md) - [Do MiSeq Wash Tubes include an expiration date?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000009678.md) - [Does MiSeq verify the number of cycles in a planned run against the cycles supported by the reagent kit?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000003094.md) - [How Long Does the Flow Rate Check Take During the MiSeq Pre Run Checks?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000009127.md) - [How much template does the MiSeq System use?](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002524.md) - [How to access MiSeq Reporter](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000003627.md) - [How to stop a MiSeq run](https://knowledge.illumina.com/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000005081.md) --- # Agent Instructions This documentation is published with GitBook. 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