ASHG 2026 UCSC Genome Browser Short Course - ASHG
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ASHG 2026 UCSC Genome Browser Short Course

$200.00

Monday, October 19 and Tuesday, October 20: Day 1 (Monday): 2pm-5pm, Day 2 (Tuesday): 9am-12pm, 1pm-3pm
Pricing: $120 ASHG member, $200 nonmember. Registration and advance ticket purchase required to attend.

*Per our policies, add-ons (ticketed events, CEUs, and any other items at an additional cost) are non-refundable, non-transferable, and non-exchangeable.

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Description

This 2-day short course is designed to give attendees a strong foundational understanding of the UCSC Genome Browser, including hands-on experience with its core functions and an introduction to its more advanced features. While not intended to create expert-level users, attendees will leave equipped with the skills and confidence needed to navigate and more effectively use the Genome Browser in their work. Attendees should bring their laptops to fully participate.

The UCSC Genome Browser has become a become an essential tool in the workflows of many people in both the clinical and research domains. A genomic-coordinate-based display allows access to data at any scale from a single nucleotide to an entire chromosome. Offering quick access to a mountain of data in an intuitive interface, the Browser has, over 25 years, continued to add new features and new data. Much like Photoshop or Excel, the Browser is used by many, but few are adept at more than a subset of the features. The underlying data vary from one genome assembly to another, but essentially, anything that can be localized to a genomic coordinate can be displayed on the Browser. These data include mRNA mappings (gene models), transcription-factor binding sites, histone- and DNA-modification locations, expression data, conservation and importantly, variants (SNVs and CNVs) both pathogenic and benign. This arrangement allows the user to pursue biological inquiries by accessing the data directly and quickly.

The workshop will feature the most useful functions of the Browser that are not obvious to the casual user. For 20 years, the presenter has taught these features in more than 350 workshops and has learned from experience which ones are most likely to be unknown to even experienced users yet provide functionality that will become essential going forward.

UCSC Genome Browser – Session 1

The first Browser short course session will present the Browser visual display paradigm and feature navigation and configuration options. Through demonstration and hands-on exercises, participants will

  • Understand the display modes: dense, squish, pack and full in several contexts. The modes vary across different data types, discussion of which serves as an introduction to several of the main data types in use in the Browser display.
  • Configure Browser-wide options to optimize their viewpoint – allowing the data to show what is important to the user.
  • Rearrange data ordering, zooming in and out and highlighting.
  • Investigate default tracks.
  • Investigate the differences among human genome assemblies, hg19, hg38, hs1 (T2T).
  • Search/Navigate the genome, using gene names, HGVS nomenclature and accession names and numbers (RefSeq, OMIM, GENCODE and more).
  • Explore right-click menu options.
  • Click into details pages for individual items in various datasets and from there to the original data sources.
  • Access Track Descriptions, which describe the data, the process of collecting and configuring it and, importantly, color conventions used in the track.
  • Explore track-specific configuration options.
  • Export .pdf images of Browser views and other output options.

Questions will be encouraged throughout.

UCSC Genome Browser – Session 2

The second Browser short course session will present more advanced features of the Browser. Through demonstration and hands-on exercises, participants will

  • Explore a variety of datasets through the Recommended Track Sets – shortcuts to enable tracks relevant to interpretation of SNVs or CNVs, including pathogenic and benign variants, genetic literature, OMIM, ClinVar, gnomAD and splice predictions.
  • Investigate multiple subtracks within composite tracks that sometimes obscure the full extent of available data.
  • Load their own data into the Browser as Custom Tracks in a variety of formats.
  • Use the Table Brower to export subsets of data from large data tables, including exporting coordinates for genes discontinuous in the genome.
  • Save sessions for future use, publication and/or sharing with colleagues (stable links).

Questions will be encouraged throughout.

UCSC Genome Browser – Session 3

The third Browser short course session will present still more advanced features of the Browser. Through demonstration and hands-on exercises, participants will

  • Appreciate Comparative Genomics datasets: Chain, Net, multiz and liftOver and use them to navigate among genomes.
  • Enable Multi-Region mode, which allows user-supplied discontinuous regions to be displayed together – including Exon-only mode.
  • Import, export and search sequences: BLAT, isPCR, Short Match and Get DNA.
  • Perform Table Browser queries with filters.
  • Download data using the Table Browser and the API.

Questions will be encouraged throughout.

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