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UCSC Genome Browser Two Day Workshop
UCSC Genome Browser Workshop
Thursday April 20 and Friday April 21
8:45 AM – 4:00 PM
Claude Moore Health Sciences Library, Multipurpose Innovation Learning Lab (MILL)
Join us for this two-day, hands-on workshop on the UCSC Genome Browser, led by Robert Kuhn PhD, Associate Director, UCSC Genome Browser.
Workshop fee of $20 includes registration and morning and afternoon breaks - NEW! sandwiches provided for lunch.
Sponsored by:
UVA Claude Moore Health Sciences Library, UVA Center for Public Health Genomics, and the UVA Cancer Center.
AGENDA
DAY 1
8:45 am - 9:00 am Coffee, Breakfast, and Welcome
9:00 am - 10:30 am Intro to the UCSC Genome Browser - features and navigation
- 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 am - 10:45 am Coffee break
10:45 am - 12:00 pm More Genome Browser - data
- A short tour of our data
- Starting points for browsing our data:
- genomic position
- sequence
- gene
- variants -- CNVs and SNPs, benign and pathogenic
- publication
- How to find more info about a track or track item
- Track groups and brief demo of our most popular data sets
- 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
- Gentle intro to the Table Browser
- Getting gene sequences using the Table Browser
- Getting track information using the Table Browser
12:00pm - 1:00 pm Lunch (sandwiches provided)
1:00 pm - 4:00 pm (includes refreshment break)
- Cementing your knowledge: Working through problem sets
- One-on-one consultation/troubleshooting
- Examples of comparative genomics, changes between assemblies, evolution
DAY 2
8:45 am - 9:00 am Coffee, Breakfast, and Welcome
9:00 am - 10:30 am Getting more out of the Browser
- 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
10:30 am - 10:45 am Coffee break
10:45 am - 12:00 pm Browsing variant data and sensitive data
- 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 pm - 1:00 pm Lunch (sandwiches provided)
1:00 pm - 4:00 pm (includes refreshment break)
- Cementing your knowledge: Advanced problem session to work on example problems
- One-on-one consultation/troubleshooting
- Using the Browser in teaching genetics and molecular biology
- Date:
- Friday, April 21, 2017
- Time:
- 8:45AM - 4:00PM
- Location:
- Health Sciences Library MILL (First Floor)
- Instructor:
- Robert Kuhn, UCSC