Analysis in ICA

Overview

This tutorial guides you through running the Illumina DRAGEN miRNA pipeline using Illumina Connected Analytics. You'll begin by setting up a project with demultiplexed instrument run data (FASTQ), adding pipelines and running a pipeline.

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Set-up

This tutorial assumes you already have an existing project in ICA. To create a new project, please see instructions in the Projects page.

Additionally, you will need the Illumina DRAGEN miRNA Bundle linked to your existing ICA project. The DRAGEN miRNA Demo Bundle is an an entitled bundle provided by Illumina with all standard ICA subscriptions and includes DRAGEN pipelines, references, and demo data.

Linking an Bundle

For general steps on creating and linking bundles to your project, see the Bundles page. This tutorial explores the DRAGEN miRNA Published Pipeline, so we will need to link the DRAGEN miRNA Bundle to our existing project.

Steps:

• Go to the Projects > your_project > Project settings > Details page

• Click Edit

• Click the + button, under Linked bundles

• Select the DRAGEN miRNA 1.0.0 Bundle, followed by Link.

• Finally, save the change.

DRAGEN miRNA 1.0.0 Bundle assets will now be available on the Data and Pipelines pages.

Pipelines

After setting up the project in ICA and linking a bundle, we can run various pipelines.

DRAGEN miRNA Published Pipeline

This example demonstrates how to run the DRAGEN_miRNA_1-0-0 Published Pipeline in your ICA project using the demo data from the linked DRAGEN miRNA 1.0.0 Bundle.

The required pipeline input assets for this tutorial include:

• Under Projects > your_project > Data

  • Illumina DRAGEN miRNA Demo Data folder

• Under Projects > your_project > Flow > Pipelines

  • Illumina DRAGEN miRNA

Launching the Illumina DRAGEN miRNA Published Pipeline with Demo Data

From the Projects > your_project > Flow > Pipelines page, select Illumina DRAGEN_miRNA_1-0-0, and then click Start analysis. Initial set-up details require pipeline run name meaningful to the user and a Subscription from the drop-down menu under Pricing.

Running the Illumina DRAGEN miRNA pipeline uses the following inputs which are to be added in the Input Files section:

FASTQ files

Select the FASTQ files in the Illumina DRAGEN Enrichment Demo Data folder and select Add.

Reference

Select the reference database to be used for mapping and annotation. The database name indicates the collection of reference files used for small RNA classification and is based on the corresponding miRBase version. Default Reference is set to "miRBase_v22".

Species

Select the species of interest. Libraries from six model organisms are available for miRNA classification. Default species is set to "Human".

Resources

Choose the expected storage space required for storing analysis results.