> 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/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list.md).

# Troubleshooting

Software > On Instrument Analysis Software > Troubleshooting

* [Creating a custom DRAGEN reference genome for NextSeq1000/2000 analysis](/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000007055.md)
* [Generate FASTQ from an incomplete run in Local Run Manager](/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](/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002415.md)
* [Troubleshooting demultiplexing issues using Local Run Manager](/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002862.md)
* [Troubleshooting demultiplexing issues using MiSeq Reporter](/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](/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](/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000009008.md)


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