Posted by & filed under Training.

This workshop is co-hosted by the Bioinformatics Training Program and the Data Intensive Biology Training Program.

Instructors: Dr. Robert Kuhn and Angie Hinrichs, UCSC

 

If you are a UC Davis School of Veterinary Medicine student or affiliate and would like to register, please contact Dr. C. Titus Brown (ctbrown@ucdavis.edu).

Otherwise, click to register:

Register

 

General Information … The UCSC Genome Browser (http://genome.ucsc.edu/) is a powerful 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.

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers. There are no prerequisites.

Where is the workshop? … It will be held in Gladys Valley Hall on the UC Davis campus and will run from 9am to 5pm on the dates indicated.

What do I need to bring? … A laptop!  The UCSC Browser works best on recent versions of Firefox, Chrome, Safari and Internet Explorer (in that order).

How much does it cost? … The registration fee is $75 and includes all workshop materials, coffee, lunch, beverages and snacks, but does not include dinner, lodging or parking fees.

How do I apply? … Registration is “first-come, first-served”. There is no application process. Half of the seats are reserved for SVM affiliates, the rest are immediately available to everyone. If any SVM-reserved seats have not been taken by November 15, they will be released to the waitlist.

Questions? … email us at bioinformatics.core@ucdavis.edu

Workshop Schedule – Day 1

Intro to the UCSC Genome Browser (beginning/novice user material)

A guided tour of the basic elements of the UCSC Genome Browser:

  • General overview of the Browser, what it is, history
  • Configuring the display
  • Track settings
  • Exporting Browser images for publication
  • Searches: for regions/positions, gene names, motifs, other keywords
  • Demo of example searches: Gene of interest, regions of interest, dataset/publication of interest
  • Saving and sharing sessions
  • Microarrays and chromosome imbalances
  • NGS sequencing data — paired ends, BAM files, variants calling/display

Uploading and displaying your data

  • Custom tracks

[break]

A short tour of our data

  • Starting points for browsing our data:
    • Genomic position
    • Sequence
    • Gene/motif
    • Variant
    • Publication
  • How to find more info about a track or track item
  • Track groups and brief demo of our most popular data sets:
    • Mapping and Sequencing
    • Genes and Gene Predictions
    • Comparative Genomics
    • Variation
  • How to download our data
    • How to get DNA for the region you are viewing
    • Intro to the Table Browser
    • Getting gene sequences using the Table Browser
    • Getting track information using the Table Browser

[Lunch]

  • Working through a problem set

Workshop Schedule – Day 2

Getting more out of the Browser

  • Table Browser advanced examples:
    • Intersection
    • Filtering
    • Finding the table that goes with your track
  • Track Hubs
    • How to make  your own track hub

[Break]

Browsing variant data and sensitive data

  • The Variant Annotation Integrator: annotation for your variants all in one place
  • Genome Browser in a Box: Hosting a local copy of the Genome Browser on your laptop

[Lunch]

Advanced problem session to work on example problems
one-on-one conversations about whatever comes up