16 June 2022 -
Level 1, 21 Bedford St. North Melbourne
Introduction to Genome Browsers
Workshop date/time (Melbourne time): Thursday 16th June 9am to 2pm Lead trainer Vicky Perreau (Melbourne Bioinformatics, The University of Melbourne) 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. 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