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UCSC Genome Browser Workshop


Penn Vet's Center for Host-Microbial Interactions (CHMI) and the Penn Institute for Immunology (IFI) are co-sponsoring a free, two-day intensive workshop on how to use the UCSC Genome Browser.

A tentative schedule for the workshop is shown below.  If you have any questions about the event, or there are topics not represented in this agenda that you would like to see covered, please contact Dan Beiting (beiting@upenn.edu).

Seating is limited, so we ask that you complete the web registration below. Priority will given to graduate and post-doctoral students that are part of Penn Vet or enrolled in the IGG or MVP graduate programs.

Dates:

  • Thursday, July 20, 2017
  • Friday, July 21, 2017

Location:

  • Hill Pavilion, Rm 130/131

Workshop Instructor:


Registration - UCSC Genome Browser Workshop

 

UCSC Genome Browser Workshop -- Thursday, July 20, 2017
When What
 8:30 - 9:00 am
 Registration
9:00 - 10:30 am Introduction 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 - 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
    • comparative genomics -- synteny and evolution
    • publication
  • 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
    • Gentle intro to the Table Browser
    • Getting gene sequences using the Table Browser
    • Getting track information using the Table Browser
12:00 - 1:00 pm
Lunch
1:00 - 4:00 pm

Cementing your knowledge: Working through problem sets

One-on-one consultation/troubleshooting

Examples of comparative genomics, changes between assemblies, evolution


UCSC Genome Browser Workshop -- Friday, July 21, 2017
When What
9:00 - 10:30 am Getting more out of the Browser

A guided tour of the basic parts of the UCSC Genome 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 - 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 - 1:00 pm
Lunch
1:00 - 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