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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:
Thursday, April 20, 2017
Time:
8:45am - 4:00pm
Location:
Health Sciences Library MILL (First Floor)
Instructor:
Robert Kuhn PhD, Associate Director, UCSC Genome Browser
Registration has closed.