KY INBRE Genome Browser Workshop

As of January 18, 2023, this website will no longer be maintained. Please visit us online from now on at our new home at kyinbre.org

Page updated November 10, 2022

You’re invited to join us for this FREE hybrid two-day hands-on workshop on The University of California Santa Cruz (UCSC) Genome Browser, an essential tool for students and researchers working in genomics and related fields. The Browser allows visualizing genomic data from RNA-seq, ChIP-seq, and other genomic datasets in more than 100 animal species.

Users can create their own "tracks" to map their own data on the genome and/or use annotated publicly available data.

No programming skills needed! This workshop is suited for both new and experienced users.  

Workshop will be held with a hybrid option. Attend virtually or attend in-person at the University of Louisville, Clinical and Translational Research Building Room 101, 505 S. Hancock St., Louisville, KY 40202 (map)

Register by January 13, 2023.

For questions or more information contact, Sabine Waigel, Assistant Director, Genomics Training and Education Core (GTEC), 

SAMPLE Agenda

DAY 1 – January 23

  • 9 to 10:30 am: Intro to the UCSC Genome Browser – features and navigation

    A tour of the basic parts of the UCSC Genome Browser: 
    • General overview of the Browser, what it is, history
    • Display configuration
    • Track settings
    • Exporting Browser .pdf images for publication
    • Searches: for regions/positions, gene names, motifs, other keywords
    • Searches: BLAT, short match track for sequences
    • Searches: PCR for primers
    • Demo of example searches: Gene of interest, regions of interest, dataset/publication of interest
    • Navigation: drag-and-zoom, drag-reorder tracks, switching genome assemblies and organisms via homology
    • Keeping track of your thinking by saving and sharing sessions

  • 10:30 to 10:45 am: Coffee Break

  • 10:45 am to 12 noon:  Genome Browser data 

    • Starting points for browsing our data: genomic position, sequence, gene, HGVS nomenclature 
    • Data types – BED files, wiggle, BAM, VCF, dbSNP 
    • More data types – barChart, interact, Hi-C, , lollipop 
    • Variants – CNVs and SNPs, benign and pathogenic 
    • Data – genesets, annotation, 1000 Genomes, GnomAD, OMIM, GTEx expression data, CRISPR guides, pathways, Epigenomics … 
    • Publications / gene interactions 
    • Proteomics 
    • How to find more info about a track or track item 
    • Variants – Understanding various SNP tracks 


More features 

    • Table Browser and extracting data 
    • Custom tracks - uploading and displaying your own data in the Browser 
    • Custom track examples – BED files. Sequences data: coverage (BAM files), variant calls (VCF), RNA-seq (wiggle) 
    • The Variant Annotation Integrator – predicting biochemical consequences of short variants 
    • Public Assembly Hubs 
    • How to download our data 
    • How to get DNA for the region you are viewing 
    • Short Match, BLAT and isPCR 
    • Getting gene sequences using the Table Browser 

 

  • 12 to 1 pm: Lunch 
  • 1 to 4 pm: Cementing your knowledge: Working through problem sets 
    • Participant-directed review of features and data 
    • One-on-one consultation/troubleshooting 
    • Examples of comparative genomics, changes between assemblies, evolution 

DAY 2 – January 24

  • 9 to 10:30 am: Getting more out of the Browser 
    • Multi-Region mode 
      • Exon-only display 
      • Viewing discontinuous regions of your choice (e.g., pathways) 
      • Alternate haplotypes in human genome assemblies 
    • Table Browser advanced examples – Intersection, Filtering 
      • Finding the table that goes with your track 
    • Data Integrator – combining data from multiple tables 
    • Track collections – co-configure multiple wiggle tracks 
    • Recommended Track Sets – interpreting variants large and small 
  • 10:30 to 10:45 am: Coffee break 
  • 10:45 am to 12 noon: Large and remote datasets and sensitive data 
    • Track Hubs, including making your own 
    • Assembly Hubs – A Browser for your genome of interest 
    • Genome Browser in a Box: Hosting a local copy of the Genome Browser on your laptop – solution for sensitive data inside your firewall 
  • 12 to 1 pm: Lunch 

  • 1 to 4 pm: Cementing your knowledge: Advanced problem session to work on example problems 
    • Participant-directed review of features and data 
    • Using the Browser in teaching genetics and molecular biology 
    • Concurrent: One-on-one consultation/troubleshooting