> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/dragen-single-cell-rna/analysis-methods/guide-rna-calling.md). # Guide RNA Calling DRAGEN now also supports guide RNA calling - identifying cells that express guide RNA sequences. Although the counts matrix reports how many feature counts were found for each cell, there is a chance that the feature reads happened to match to the feature barcode reference sequence or the feature count was assigned to the cell by chance rather than due to real signal. Guide RNA calling applies an additional filtering step to distinguish between cells truly expressing guide RNA sequences and noise (similar to how cell filtering is performed to distinguish true passing cells from noise) For more information on Guide RNA calling refer to the DRAGEN User Guide detailing the Gaussian Mixture Model approach: [DRAGEN v4.6](https://help.dragen.illumina.com/dragen-v4.6/product-guides/dragen-v4.6/dragen-single-cell-pipeline/dragen-scrna-illumina#guide-rna-calling) or [DRAGEN v4.5](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-illumina#guide-rna-calling). --- # 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 by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/dragen-single-cell-rna/analysis-methods/guide-rna-calling.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. 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.