UCSC Genome Browser Workshop

Date: 
February 14, 2020
Time: 
9am - 5pm
Place: 
Genentech Hall - Byers Auditorium

UCSC Genome Browser Workshop

February 14 @ 9:00 am - 5:00 pm

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.

Note: Main Session in Byers Auditorium, 9:00am-12:00pm; Hands-on Workshop in MH 1407, 1:00-5:00pm
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
  • 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 tracksMore 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 Collections2:00 – 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
  • Eventbrite link: https://www.eventbrite.com/e/ucsc-genome-browser-workshop-tickets-89175826297