Introduction to Genome Browsers

Introduction to Genome Browsers.

Lead trainer: Vicky Perreau

(Melbourne Bioinformatics, The University of Melbourne)

Workshop Description:

This hands on tutorial on Genome Browsers will provide beginners with an introduction to both the UCSC Genome browser and IGV (Integrative 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.

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
• Use the 'Blat' tool to locate genomic regions with similarity to a sequence of interest.
• Create custom interactive views with to share with colleagues
• Generate images for publications.
• Download BAM files from SRA and view RNA-Seq alignments in in IGV.

Workshop delivery environment:

Interacting with the UCSC genome browser web based platform and locally installed IGV.

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 if Melbourne and its affiliated institutes.

You must register for this event using an affiliated institutional email address or your registration may be cancelled.

Prerequisites and Requirements

This is an in person hands-on workshop and attendees must bring their own computers with access to the Uniwireless or Eduroam internet/wifi. 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 (Integrative Genome Viewer) (free)
• Obtain a login to UCSC Genome browser (free)

Access

If you require any further information, or have any access requirements in order to participate in this workshop, please contact us as soon as possible to discuss your requirements:

We recommend that following our eventbrite page if you wish to be alerted when we release new workshops for registrations. If you require any further information, please contact Melbourne Bioinformatics at:

bioinformatics-training@unimelb.edu.au