# 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><img src="https://665610505-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FRvUv32d8wOzBh0okiOjK%2Fuploads%2Fgit-blob-e15e03004f85a77587e48d161a3026d74bf2def9%2FScreenshot%202025-09-09%20at%202.06.12%E2%80%AFPM.png?alt=media" alt=""><figcaption><p>Figure 1. Illumina miRNA prep E2E worfklow.</p></figcaption></figure>

#### 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](https://help.connected.illumina.com/dragen-mirna/tertiary-analysis/illumina-connected-multiomics) section for additional details.


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