# Analysis in BSSH

### Overview

This tutorial guides you through running the Illumina DRAGEN miRNA pipeline using [BSSH](https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub.html). You’ll begin by setting up a project with demultiplexed sequencing data (FASTQ files), selecting the DRAGEN miRNA app and launching an analysis run.

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### Set-up

This tutorial assumes you already have an existing project in BaseSpace.

If you do not yet have a project:

* Create a new project from the **Projects** page in BaseSpace.
* Upload or import demultiplexed FASTQ files into the project.

You will also need access to the DRAGEN miRNA App. This app is typically available through your BaseSpace subscription or via your organization’s licensed apps.

### Preparing Your Project

#### Uploading or Importing Data

1. Go to **Projects** in BaseSpace.
2. Open your target project.
3. Upload FASTQ files or import them from an instrument run or external storage.
4. Confirm that all required FASTQ files appear in your project’s **Samples/Data** section.

### Apps

After setting up your project and data, you can run analysis apps.

#### DRAGEN miRNA App

This example demonstrates how to run the DRAGEN miRNA app in your BaseSpace project using your uploaded FASTQ data.

Required inputs:

* FASTQ files stored in your BaseSpace project
* A reference database
* Species selection

### Launching the DRAGEN miRNA App

1. From your project page, click on the rocket icon (or go to the **Apps** tab).
2. Search for and select **DRAGEN miRNA**.
3. Click **Launch App**.

#### **Initial Setup**

You will be prompted to:

* Enter a meaningful **analysis name**
* Select a **project** for output storage
* Confirm your **compute/subscription** options (if applicable)

**Input Configuration**

In the app configuration screen, provide the following inputs:

**FASTQ/Biosample Files**

* Select the FASTQ files from your project.
* Add them to the input section.

**Reference**

* Choose the reference database for mapping and annotation.
* The reference corresponds to a miRBase version.
* Default reference is typically **miRBase\_v22**.

**Species**

* Select the organism of interest.
* Supported model organisms are available in a dropdown list.
* Default species is **Human**.

**Analysis Output**

Choose the project where your analysis results should be saved.

### Running the Analysis

1. Review all configuration settings.
2. Click **Launch Application**.
3. Monitor progress from the **Runs** or **Analysis** dashboard.

#### **Launching the Illumina DRAGEN miRNA Published Pipeline with Demo Data**

To run DRAGEN miRNA using Illumina demo data, follow these steps:

1. **Add Demo Data:**
   * Navigate to the **Demo Data** tab in your BaseSpace Sequence Hub (BSSH) dashboard.
   * Search for "MiSeq i100: Illumina miRNA Prep."
   * Select and import the "Project", choose the context to accept the invite, and click **Accept**.
2. **Data Processing:**
   * The demo project contains data already processed through BCLConvert (FASTQ).
   * Proceed to analyze the FASTQs with DRAGEN miRNA by following the above steps.