Workshop Description
Established in 2000, the UCSC Genome Browser is great tool for visualizing your data alongside a ton of data from all over the place. The Genome Browser now features a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. QCB Collaboratory hosts a workshop, conducted by Dr. Robert Kuhn, that is tailored to the specific needs and skill levels of our audience
Day 1
9:00 – 10:30 Intro to the UCSC Genome Browser – features and navigation – Boyer 529
A guided tour of the basic parts of the UCSC Genome Browser:
* General overview of the Browser, what it is, history
* Display configuration
* Track settings
* Exporting Browser images for publication
* Searches: for regions/positions, gene names, motifs, other keywords
* Searches: BLAT, short match track for sequences
* Searches: PCR for primers
* Demo of example searches: Gene of interest, regions of interest, dataset/publication of interest
* Navigation: drag-and-zoom, drag-reorder tracks, switching genome assemblies and organisms via homology
* Keeping track of your thinking by saving and sharing sessions
10-30 – 10:45 Coffee break
10:45 – 12:00 More Genome Browser – data – Boyer 529
A short tour of our data
* Starting points for browsing our data:
* genomic position
* sequence
* gene
* HGVS nomenclature
* data types
* variants — CNVs and SNPs, benign and pathogenic
* comparative genomics — synteny and evolution
* publications / gene interactions
* proteomics
* How to find more info about a track or track item
* Table Browser and extracting data
* Custom tracks – uploading and displaying your own data in the Browser
* Custom track examples – BED files. Sequences data: coverage (BAM files), variant calls (VCF), RNA-seq (wiggle)
* Public Assembly Hubs
* How to download our data
* How to get DNA for the region you are viewing
* Getting gene sequences using the Table Browser
12:00 – 1:00 Lunch
1:00 – 4:00 – Boyer 130
Cementing your knowledge: Working through problem sets
One-on-one consultation/troubleshooting
Examples of comparative genomics, changes between assemblies, evolution
Day 2
9:00 -10:30 Getting more out of the Browser – Boyer 529
* Multi-Region mode
* Exon-only display
* Viewing regions of your own choice, including discontinuous (e.g., pathways)
* Alternate haplotypes in human genome assemblies
* Public sessions – sharing your data with everyone
* Table Browser advanced examples:
* Intersection
* Filtering
* Finding the table that goes with your track
* Track Hubs
* How to make your own track hub
* Assembly Hubs
* Make a track hub for your genome of interest
* New feature: Track collections
10-30 – 10:45 Coffee break
10:45 – 12:00 Browsing variant data and sensitive data – Boyer 529
* Understanding various SNP tracks
* The Variant Annotation Integrator: predicting biochemical consequences of short variants
* Genome Browser in a Box: Hosting a local copy of the Genome Browser on your laptop
* GBiB as Browser inside your firewall
* Using GBiB and Assembly hubs to explore sensitive data
12:00 – 1:00 Lunch
1:00 – 3:30 – Boyer 130
Cementing your knowledge: Advanced problem session to work on example problems
One-on-one consultation/troubleshooting
Using the Browser in teaching genetics and molcular biology
Technical Requirements
- We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.
Instructor
Robert Kuhn, Ph.D. is the Associate Director of the Genome Browser at the University of California, Santa Cruz. Dr. Kuhn earned his PhD in Biochemistry and Molecular Biology at UC Santa Barbara.
Dr. Kuhn conducts trainings and workshops on how to use the Browser and its associated bioinformatics tools. He has been interacting with the medical genetics community to acquire useful datasets for the Browser and to learn about how to make it more useful to the scientific community.
Email: kuhn@soe.ucsc.edu
Website: http://genome.ucsc.edu
Workshop Details
Prerequisites: None.
Length: 2 days, 6-7 hrs per day
Level: Intermediate
Location: Collaboratory Classroom (Boyer Hall, 529) (mornings); Sigman Room (Boyer Hall, 130) (afternoons)
Seats Available: 28
Fall 2018 Dates
November 13 and 14, 2018
9:00 AM – 4:00 PM