> 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/dragen-mirna/readme.md).
# Introduction
The DRAGEN miRNA software is integral to the Secondary Analysis step in Illumina's miRNA prep End-to-End (E2E) solution, accessible via the BaseSpace Sequence Hub (BSSH) and Illumina Connected Analytics (ICA) cloud platforms. This section aims to illustrate how counts align within the workflow and to outline the other components of the E2E solution (see Figure 1).
Figure 1. Illumina miRNA prep E2E worfklow.
#### Illumina miRNA E2E workflow
After preparing samples with the Illumina miRNA Prep kit, customers can create a Sample Sheet during the **BSSH Run Planning** step and upload or select it on the **sequencer**.
Once sequencing is complete, they can demultiplex the data using the **BCLConvert** app in BSSH or a local installation to generate FASTQ files.
These FASTQs are then used for secondary analysis (DRAGEN miRNA app), which produces small RNA count matrices, mapping statistics, and a full Quality Control **DRAGEN Report**.
Final outputs, including count matrices and DRAGEN Report, can be downloaded from BaseSpace or **ICA**, depending on the customer’s subscription.
Customers can perform tertiary analyses—such as differential expression analysis—using Illumina Connected Multiomics. Refer to the[ Illumina Connected Multiomics](/dragen-mirna/tertiary-analysis/illumina-connected-multiomics.md) section for additional details.
---
# 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.connected.illumina.com/dragen-mirna/readme.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.
