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UCSC Genome Browser Workshop
May 4, 2021 @ 9:00 am - 12:00 pm
The UCSC Genome Browser is a powerful web-based tool for interacting with genome assemblies of many organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments.
Prior experience with the Browser is not necessary for attendees, though it is recommended, as the instruction will progress to cover some more advanced topics.
Two Day Workshop, 9 am – 12 pm
May 4th – Lecture
May 5th- Hands-on session
Workshop Agenda
May 4th
9:00 – 10:30am Intro to the UCSC Genome Browser – features and navigation.
An abbreviated tour of the basic parts of the UCSC Genome Browser, highlighting the latest data:
• General overview of the Browser, what it is, history
• Display configuration
• Navigation: drag-and-zoom, drag-reorder tracks, switching genome assemblies and organisms via homology
• Demo of example searches: Gene of interest, regions of interest, dataset/publication of interest
• Data – genesets, annotation, 1000 Genomes, GnomAD, OMIM, GTEx expression data, CRISPR guides, histone modification, pathways
• Exporting Browser .pdf images for publication
• Keeping track of your thinking by saving and sharing sessions
• Custom tracks – uploading and displaying your own data in the Browser
10:30 – 10:45am Break
10:45 – 12:00 Genome Browser data
• Data types – BED files, wiggle, BAM, VCF
• Variants – CNVs and SNPs, benign and pathogenic
• Comparative genomics – homology, synteny and evolution
• Publications / gene interactions
• Variants – Understanding various SNP tracks
More features
• Table Browser and extracting data
• Multi-region views: exon-only mode, and viewing discontinuous regions
• The Variant Annotation Integrator – predicting biochemical consequences of short variants
• Assembly Hubs
• How to get DNA for the region you are viewing
• Short Match, Get DNA and isPCR
May 5th
9:00 – 10:00am Track Hubs and Track Collections
• Multi-Region mode
• Exon-only display
• Viewing discontinuous regions of your choice (e.g., pathways)
• Table Browser advanced examples – Intersection, Filtering
Finding the table that goes with your track
• Loading large datasets using track hubs
• Co-configuring RNA-seq and other wiggle data using Track Collections
10:00am – 12:00pm Cementing your knowledge: Working through problem sets
• Example problems to highlight Browser features and stimulate thinking about how to use the Browser
