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UCSC Genome Browser
gateway to whole-genome data

Instructor: Robert Kuhn, PhD

Friday, January 31, 2020

Location
Carmichael Building
Michelle Winn Memorial Conference Room, Bay 47, Room 215
300 North Duke Street, Durham, NC 27701

Agenda (register at the bottom of this page)

8:30 AM to 10:00 AM - Introduction to the UCSC Genome Browser.

  • General overview of the Browser, what it is, history
  • A guided tour of the basic parts of the UCSC Genome Browser
  • Navigation, including between organisms by homology, zooming and panning; configuring track visibility
  • Data – genesets, annotation, Comparative Genomics, GTEx expression data, CRISPR guides, pathways, Gene Interactions.
  • Searches: for regions/positions, gene names, motifs, HGVS, other keywords, BLAT, short match track for sequences
  • Saving/Retrieving/Sharing sessions
  • Custom tracks – loading your own data -- new formats: interact, Hi-C, and lollipop
  • Export to .pdf

10:00 AM to 10:20 AM - Break

10:20 AM to 12:00 PM - Advanced Browser topics.

  • Finding data
  • Variants – benign/pathogenic and CNVs/SNVs
  • Table Browser – extracting data from tables
  • Track Hubs – remotely hosted data
  • Multi-region:  exon-only display, defined regions
  • Get DNA and use for PCR primers (in-silico PCR)
  • RNA-seq and Track Collections – co-configuration of datasets

12:00 PM - 1:00 PM Lunch Break

1:00 PM to 2:00 PM

  • Follow-up and questions

2:00 PM to 2:20 PM - Break

2:20 PM to 4:30 PM - working through problem sets

*Participants should bring a fully charged laptop.*

A maximum of 30 attendees will be allowed.