# On Instrument Analysis Software

- [Reference Material](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list.md)
- [Allowed characters for Run Names and Sample IDs in Local Run Manager v3](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005750.md)
- [Comparison of MiSeq Reporter and Local Run Manager analysis workflows](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005974.md)
- [Connecting remotely to Local Run Manager v4 on instrument](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000002323.md)
- [How to Specify Adapters for Trimming in Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000003678.md)
- [How to add a Custom Reference Genome in Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000002685.md)
- [How to generate FASTQ files for index reads in MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001326.md)
- [How to generate FASTQ files from an incomplete run in MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001325.md)
- [How to requeue analysis of a run with MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001782.md)
- [How to set up an AmpliSeq for Illumina run using Local Run Manager v1.3 for MiniSeq](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000002952.md)
- [How to use a custom library prep kit in Local Run Manager v2](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001317.md)
- [How to use custom library prep and index kits with Local Run Manager v3 and v4](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005897.md)
- [Local Run Manager How to create FASTQ files for index reads](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001323.md)
- [Local Run Manager v3 with MiSeq Control Software v4 Introduction Support Webinar Video](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000008078.md)
- [Local Run Manager 如何利用不完整的测序结果生成FASTQ文件](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007112.md)
- [Using Illumina Experiment Manager (IEM) to Create a Sample Sheet for Illumina Libraries Video](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005856.md)
- [如何使MiSeq Reporter生成Index Reads 的FASTQ文件](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007352.md)
- [如何使用MiSeq Reporter从未完成的run中创建出FASTQ文件](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007401.md)
- [如何使用MiSeq Reporter重新分析一个run？](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007342.md)
- [如何在Local Run Manage中进行重分析（Requeue）及导入运行数据（Import）再分析](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007141.md)
- [如何将桌面测序仪和Local Run Manager与网络存储位置进行连接](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007367.md)
- [FAQ](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list.md)
- [Can a run be started on the NovaSeq X/X Plus while an analysis is ongoing?](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list/000008267.md)
- [Can the MiSeq System generate FASTQ files?](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list/000002606.md)
- [MiSeq Reporter Common Questions](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list/000002240.md)
- [Troubleshooting](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list.md)
- [Creating a custom DRAGEN reference genome for NextSeq1000/2000 analysis](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000007055.md)
- [Generate FASTQ from an incomplete run in Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000001807.md)
- [How to remove a BCL file from analysis in MiSeq Reporter or Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002415.md)
- [Troubleshooting demultiplexing issues using Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002862.md)
- [Troubleshooting demultiplexing issues using MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002227.md)
- [Troubleshooting demultiplexing issues using onboard DRAGEN on the NextSeq 1000/2000](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000003817.md)
- [Unlocking an account or resetting the password on Local Run Manager version 4](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000009008.md)


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