Event box

UCSC Genome Browser Two Day Workshop

A two-day, hands-on workshop on the UCSC Genome Browser.

Workshop fee of $20 includes registration and morning and afternoon breaks (lunch is on your own).

To register for this event, please complete these two steps:

1. Register at http://cal.hsl.virginia.edu/event/3057153.

2. Complete payment via the Health Sciences Library Events page.

AGENDA

DAY 1

8:30 am - 9:00 am Registration and Coffee

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

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 on your own

1:00 pm - 4:00 pm

  • Cementing your knowledge:  Working through problem sets
  • One-on-one consultation/troubleshooting
  • Examples of comparative genomics, changes between assemblies, evolution

 

DAY 2

8:30 am - 9:00 am Registration and Coffee

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 am 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 on your own

1:00 pm - 4:00 pm

  • 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

Sponsored by:

UVA Claude Moore Health Sciences Library ~ UVA Center for Public Health Genomics ~ UVA Cancer Center

 

Date:
Friday, April 21, 2017
Time:
8:45am - 4:00pm
Location:
Health Sciences Library MILL (First Floor)
Instructor:
Robert Kuhn, UCSC