Workshop Description

The UCSC Genome Browser is a widely used visualization tool giving access to the genomes of human and more than one hundred other animals. Dr. Kuhn’s responsibilities include identifying important datasets for inclusion into the Browser, enabling researchers through teaching the Genome Browser in workshops and seminars and learning from them how to improve the Browser.

Workshop Materials

  • 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 – GTEx, gnomAD, SNPs
  • Searches: for regions/positions, gene names, motifs, HGVS, keywords
  • BLAT, short match track for sequences
  • Saving/Retrieving/Sharing sessions
  • Export to .pdf
  • Finding data – metagenomics, transcription-factor binding sites
  • Custom tracks – loading your own data
  • Problem set and questions
  • Get DNA and use for PCR primers (in silico PCR)
  • Variants – benign/pathogenic and CNVs/SNPs
  • Table Browser – extracting data from tables
  • Multi-region: exon-only display, defined regions
  • Pathways, Gene Interactions
  • Publications – by DNA data-mining
  • Track Hubs – remotely hosted data
  • Problem set and questions
  • Data – GTEx transcript-specific expression, CRISPR guides
  • Browser conventions – naming genomes
  • Multi-region: substituting alternate haplotypes
  • Making links to the Browser
  • Conservation – chain and net tracks and multiz
  • New data types for custom tracks – interact, barChart, lollipop, Hi-C
  • RNA-seq and Track Collections – co-configuration of datasets
  • Problem set and questions

Technical Requirements

Please bring a fully charged laptop.

Instructor

Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz. He joined the UCSC Genome Browser project in 2003, where he is now Associate Director, with a particular interest in clinical genetics.

Videos

Reviews

Fantastic course, lucky to have an instructor come to visit UCLA!
Winter 2020 Student

This has been a great experience, it was very easy to follow and the instructor was phenomenal! I learned a lot and I feel much more comfortable opening a terminal and learning how to work with it now.

Winter 2020 Student
I appreciate greatly that this course is offered for free. It is incredibly helpful for graduate students who may not have studied coding in past work, but want to leverage computation to advance our research. Thanks!
Winter 2020 Student
It’s a great workshop. Highly recommend for whoever wants to learn -omics analysis without any programming background!
Winter 2020 Student

It was great! I have learned a lot!

Winter 2020 Student

Workshop Details

Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Winter 2020 Dates

February 4, 5, and 6, 2020
1:30 PM-4:30 PM

REGISTRATION IS NOW CLOSED!