Analysis in BSSH

Overview

This tutorial guides you through running the Illumina DRAGEN miRNA pipeline using BSSH. 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.