Introduction to Genome Browsers – online (note revised date)

Visualisation gives you answers to questions you didn’t know you had – Ben Schneiderman

Workshop Outline

This hands on tutorial on Genome Browsers will provide beginners with an introduction to both the UCSC Genome browser and IGV (Integrated Genome Viewer) using RNAseq gene expression data. Tools and public datasets will be used to illustrate how the expression of transcript variants can be investigated in different tissues and cell types using public data, including human RNAseq data from GTEX and mouse cell type RNAseq data from Tabula Muris, as viewed within the UCSC genome browser. A subset of aligned reads from the single cell RNAseq data Celltax study from the Allen Brain Atlas will also be downloaded from the SRA database and visualised in IGV. The data and genes used in this workshop focus on gene expression data taken from the neuroscience domain, however the analysis tools and visualizations demonstrated in this workshop can be applied to many research areas.

Trainer

Vicky Perreau, Training Lead & Senior Bioinformatician, Melbourne Bioinformatics

Learning objectives

At the end of the workshop, you will be able to:

• understand gene model representations and identify differences between transcripts variants
• investigate tissue/cell type expression profiles for genes in mouse and human gene expression data
• know some basic files types used in Genome browsers
• download BAM files from SRA and view in IGV
• use the ‘Blat’ tool to locate genomic regions with similarity to a sequence of interest
• create custom interactive views with multiple datatypes to share with colleagues and generate images for publications.

Target audience

The workshop is aimed at bench researchers with no coding/programming skills who wish to learn how to utilise online data and resources to refine their biological research questions and discovery.

Eligibility

This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section). Required: This is a hands-on workshop delivered via Zoom and attendees must use their own computers with access to the internet/wifi. We will be interacting with the web-based UCSC genome browser platform and locally installed IGV. A mouse is recommended for selecting screen elements during the workshop. The following software must also be preinstalled:

• web browser (Firefox or Chrome recommended)
• IGV (Integrated Genome Viewer) (free)
• obtain a login to UCSC Genome browser (free)
• Zoom (recently updated Version)

If you require any further information, or if you have any access requirements in order to participate in this workshop, please email us.