> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/quantifying-to-an-annotation-model.md). # Quantifying to an annotation model RNA-Seq uses the number of sequencing reads per gene or transcript to quantify gene expression. Once reads are aligned to a reference genome, we need to assign each read to a known transcript or gene to give a read-count per transcript or gene. * Click the **Aligned reads** data node * Click **Quantification** in the task menu We will use Partek E/M to quantify reads to an annotation model in this tutorial. For more information about the other quantification options, please see the [Quantification](/partek/partek-flow/user-manual/task-menu/quantification.md) user guide. * Click **Quantify to an annotation model (Partek E/M)** (Figure 1)

Figure 1. Invoking Quantify to an annotation model (Partek E/M)

We will use the default options for quantification. To learn more about the different options, please see the [Quantify to annotation model (Partek E/M)](/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-annotation-model-partek-em.md) user guide. * Choose Ensembl Transcripts release 105 annotation from the Annotation model drop-down menu (you may need to download it first, via [Library File Management](/partek/partek-flow/user-manual/settings/components/library-file-management/library-file-management-page.md) or click *Add annotation model* from the bottom of the drop-down) * Click **Finish** (Figure 2)

Figure 2. Configuring Quantify to annotation model (Partek E/M)

The Quantify to annotation model task node outputs two data nodes, Gene counts and Transcript counts (Figure 3).

Figure 3. The Quantify to annotation model task produces annotation model dependent outputs (e.g. Gene counts and Transcript counts node)

To view the results of quantification, double-click an output data node to view the task report. The task report details the number of reads within exons, introns, and intergenic regions. For detailed information about the quantification results, see the [Quantify to annotation model (Partek E/M)](/partek/partek-flow/tutorials/bulk-rna-seq/quantifying-to-an-annotation-model.md) user guide. ## Additional Assistance If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support. --- # 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://help.connected.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/quantifying-to-an-annotation-model.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.