Workshop Description
The UCSC Genome Browser is a widely used visualization tool giving access to the genomes of human and more than one hundred other animals. Dr. Kuhn’s responsibilities include identifying important datasets for inclusion into the Browser, enabling researchers through teaching the Genome Browser in workshops and seminars and learning from them how to improve the Browser.
Workshop Materials
Day 1
- General overview of the Browser, what it is, history
- A guided tour of the basic parts of the UCSC Genome Browser
- Navigation, including between organisms by homology, zooming and panning; configuring track visibility
- Data – genesets, annotation – GTEx, gnomAD, SNPs
- Searches: for regions/positions, gene names, motifs, HGVS, keywords
- BLAT, short match track for sequences
- Saving/Retrieving/Sharing sessions
- Export to .pdf
- Finding data – metagenomics, transcription-factor binding sites
- Custom tracks – loading your own data
- Problem set and questions
Day 2
- Get DNA and use for PCR primers (in silico PCR)
- Variants – benign/pathogenic and CNVs/SNPs
- Table Browser – extracting data from tables
- Multi-region: exon-only display, defined regions
- Pathways, Gene Interactions
- Publications – by DNA data-mining
- Track Hubs – remotely hosted data
- Problem set and questions
Day 3
- Data – GTEx transcript-specific expression, CRISPR guides
- Browser conventions – naming genomes
- Multi-region: substituting alternate haplotypes
- Making links to the Browser
- Conservation – chain and net tracks and multiz
- New data types for custom tracks – interact, barChart, lollipop, Hi-C
- RNA-seq and Track Collections – co-configuration of datasets
- Problem set and questions
Technical Requirements
Chrome or Firefox Internet Browser is recommended.
Instructor
Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz. He joined the UCSC Genome Browser project in 2003, where he is now Associate Director, with a particular interest in clinical genetics.
Reviews
This has been a great experience, it was very easy to follow and the instructor was phenomenal! I learned a lot and I feel much more comfortable opening a terminal and learning how to work with it now.
It was great! I have learned a lot!
Workshop Details
Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Introductory
Location: ZOOM
Seats Available: N/A
Spring 2023 Dates
May 23, 24, and 25
9:00 AM – 12:00 PM
REGISTRATION IS OPEN!
