> 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/general/software-general-troubleshooting-list.md). # Troubleshooting Software > General > Troubleshooting * [Creating custom reference genomes (non-human) to use with DRAGEN apps on BaseSpace Sequence Hub](/software/general/software-general-troubleshooting-list/000007488.md) * [DRAGEN reference differences for on-instrument and standalone analysis](/software/general/software-general-troubleshooting-list/000009589.md) * [How to demultiplex an incomplete run using bcl2fastq2 and BCL Convert](/software/general/software-general-troubleshooting-list/000003577.md) * [How to generate FASTQs from an incomplete run in Local Run Manager](/software/general/software-general-troubleshooting-list/000001807.md) * [How to troubleshoot Local Run Manager (LRM) analysis module not available at run start on NextSeq 500/550](/software/general/software-general-troubleshooting-list/000001904.md) * [How to troubleshoot a "None of the specified endpoints were reachable" error in Local Run Manager](/software/general/software-general-troubleshooting-list/000001217.md) * [How to troubleshoot barcode collision and not enough hamming distance errors when demultiplexing runs with BCL Convert and bcl2fastq2](/software/general/software-general-troubleshooting-list/000002326.md) * [Options for demultiplexing libraries with different index lengths in the same sequencing run](/software/general/software-general-troubleshooting-list/000005982.md) * [Sample specific nucleotide error bias estimation filter and systematic noise filter in DRAGEN](/software/general/software-general-troubleshooting-list/000006989.md) * [Troubleshoot issues connecting to a kernel in Illumina BioInsight Platform Core Bench Workspace](/software/general/software-general-troubleshooting-list/000007769.md) * [Troubleshooting Illumina BioInsight Platform Core Service Connector not connected for Windows computer](/software/general/software-general-troubleshooting-list/000008566.md) * [Troubleshooting demultiplexing issues for local DRAGEN analysis onboard the NextSeq 1000/2000](/software/general/software-general-troubleshooting-list/000003817.md) * [Troubleshooting demultiplexing issues using BaseSpace Sequence Hub and bcl2fastq2 v2.17+](/software/general/software-general-troubleshooting-list/000002875.md) * [Troubleshooting demultiplexing issues using MiSeq Reporter](/software/general/software-general-troubleshooting-list/000002227.md) --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://knowledge.illumina.com/software/general/software-general-troubleshooting-list.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.