Introduction to Genome Browsers
“Visualization gives you answers to questions you didn’t know you had.” – Ben Schneiderman
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.
Lead trainer: Vicky Perreau
(Melbourne Bioinformatics, The University of Melbourne)
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:
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.
This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section).
You must register for this event using an affiliated institutional email address or your registration may be cancelled.
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)
If you require any further information, or have any access requirements in order to participate in this workshop, please contact the workshop organiser Melbourne Bioinformatics as soon as possible to discuss your requirements: