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The UCSC Genome Browser is an invaluable resource both for obtaining public sequencing data and for visualizing it.Tip

Tip

Sometimes the UCSC Genome Browser at http://genome.ucsc.edu/ is pretty slow -- after all, it's a resource shared among the Eukaryotic genomics community.

But there's also a second "Beta test" version of the browser at http://hgwdev.cse.ucsc.edu/. It has slightly newer (and possibly less stable) code, but fewer people use it.

Expand
Explore UCSC Genome Browser tracks
Explore UCSC Genome Browser tracks
  • http://genome.ucsc.edu/ Genome Browser, submit
    • select Genomes →  Human GRCh38/hg38
  •  navigationnavigaion
    • type GAPDH in gene search box, jump go, then select the 1st GAPDH link.
    • note zoom out/zoom in buttons; click on position or click/drag
    track detail
    • click "Simply Nucleotide Polymorphisms (dbSnp build 130)" to expand track detail
    • click on one of the SNP to expand track detailthen click on the snp name to see details
  • selecting/hiding tracks
    • under "Regulation" section, change "ENCODE Regulation" track from "show" to "hide", refresh
    • right click "Multiz Alignments", hide
    • under "Phenotype and Disease Association" change GWAS Catalog from "hide" to "squish",  refresh
  • track detail
    • click "Simple Nucleotide Polymorphisms (dbSnp build 130)" to expand track detail
    • click on one of the SNP to expand track detail
      • then click on the snp name to see details
  • type PRNP in gene box, jump. 
    • click on "NHGRI Catalog..." track description to expand detail
    • note correspondence between SNPs (SNP 132) and disease SNPs (GWAS)
    • click on one of the disease SNPs for detail

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  1. Directly upload a data file, in one of the supported formats.
    • Your data is copied over the Internet to UCSC, where it is stored in tables and displayed as you browse.
    • Appropriate for small to medium size files (up to a few MB).
  2. Host your data locally, and configure the UCSC Genome Browser with its URL.
    • Your data resides in a location accessible via an HTTP or FTP public URL (e.g., our /corral- corral.tacc.utexas.edu:/gpfs/corral3/repl/utexas/BioITeamBioinformaticsResource/web directory, that maps to http://).
      • No data is copied to UCSC. You only tell the browser where to find the data when it is needed.
    • Appropriate for large data sets (e.g. BAM files) that can be indexed for fast retrieval.

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