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Location

UCSF Mission Bay Campus

600 16th Street

Byers Auditorium, GH 106

San Francisco, CA 94158

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Event description
UCSC Genome Browser Workshop

About this Event

The UCSC Genome Browser is a powerful web-based tool for interacting with genome assemblies of many organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments.

The main morning session, held in Byers Auditorium, will feature a tutorial on UCSC Genome Browser essentials. The afternoon session, held in Mission Hall 1407, will feature more in-depth, hands-on training and is limited to a smaller number of participants.

Prior experience with the Browser is not necessary for attendees, though it is recommended, as the instruction will progress to cover some more advanced topics. Overall, instruction for the workshop will be at the intermediate level.

Agenda

Light breakfast served at 8:30am

Main Session (9am - 12pm in Byers Aud., Genentech Hall)

9:00 - 10:30am Intro to the UCSC Genome Browser – features and navigation.

An abbreviated tour of the basic parts of the UCSC Genome Browser, highlighting the latest data:

  • General overview of the Browser, what it is, history
  • Display configuration
  • Navigation: drag-and-zoom, drag-reorder tracks, switching genome assemblies and organisms via homology
  • Demo of example searches: Gene of interest, regions of interest, dataset/publication of interest
  • Data – genesets, annotation, 1000 Genomes, GnomAD, OMIM, GTEx expression data, CRISPR guides, histone modification, pathways
  • Exporting Browser .pdf images for publication
  • Keeping track of your thinking by saving and sharing sessions
  • Custom tracks - uploading and displaying your own data in the Browser

10-30 - 10:45 Break

10:45 - 12:00 Genome Browser data

  • Data types – BED files, wiggle, BAM, VCF
  • Variants – CNVs and SNPs, benign and pathogenic
  • Comparative genomics – homology, synteny and evolution
  • Publications / gene interactions
  • Variants – Understanding various SNP tracks

More features

  • Table Browser and extracting data
  • Multi-region views: exon-only mode, and viewing discontinuous regions
  • The Variant Annotation Integrator – predicting biochemical consequences of short variants
  • Assembly Hubs
  • How to get DNA for the region you are viewing
  • Short Match, Get DNA and isPCR

Hands-on Session* (1pm - 5pm, boxed lunch provided at 12N @ MH 1407)

1:00 - 2:00 Track Hubs and Track Collections

  • Multi-Region mode
    • Exon-only display
    • Viewing discontinuous regions of your choice (e.g., pathways)
  • Table Browser advanced examples – Intersection, Filtering
  • Finding the table that goes with your track

  • Loading large datasets using track hubs
  • Co-configuring RNA-seq and other wiggle data using Track Collections

2:00 - 5:00 Cementing your knowledge: Working through problem sets

  • Example problems to highlight Browser features and stimulate thinking about how to use the Browser
  • One-on-one consultation/troubleshooting

*Please bring your own laptop and charger

Date and Time

Location

UCSF Mission Bay Campus

600 16th Street

Byers Auditorium, GH 106

San Francisco, CA 94158

View Map

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