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UCSC Genome Browser advanced topics

Tutorial and training materials by OpenHelix

Learn to use the advanced features, including the Table Browser and custom tracks, of the UCSC Genome Browser with this free tutorial, sponsored by UCSC Genome Bioinformatics Group. The UCSC Genome Browser provides a way to query and extract the data from many genomes, with extensive annotation for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more. Obtain large lists of genes, SNPs, or any other features of interest, or display your own data, using the tools underlying the UCSC Genome Browser. This tutorial is the second in a series of tutorials on the UCSC Genome Browser and explores many aspects beyond the basic search and analysis functions covered in the introductory tutorial.
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You'll learn:

  • to perform advanced searches of the UCSC genome databases
  • to export and download large quantities of targeted data
  • to create custom tracks resulting from your advanced searches
  • to create custom annotation tracks of your data to share with others
  • to use the Genome Graphs tool for visualizing GWAS data


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This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:

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Hemmat Morteza et al., Short stature, digit anomalies and dysmorphic facial features are associated with the duplication of miR-17 ~ 92 cluster. Molecular Cytogenetics (2014) doi:10.1186/1755-8166-7-27

Durdiaková Jaroslava et al., Single nucleotide polymorphism rs6716901 in SLC25A12 gene is associated with Asperger syndrome. Molecular Autism (2014) doi:10.1186/2040-2392-5-25

Petersen Britt-Sabina et al., Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-564

Tiwari Sarika et al., Histone deacetylase expression patterns in developing murine optic nerve Neural development. BMC Developmental Biology (2014) doi:10.1186/1471-213X-14-30

Londin R Eric et al., The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome Non-coding DNA and RNA. Biology Direct (2014) doi:10.1186/1745-6150-9-3

More about the resource:

The UCSC Genome Browser, sometimes referred to as the "Golden Path" browser, offers a well-organized and user-friendly view of the human genome, and dozens of other genomes as well. The official genomic sequence is supplemented with many other data types which are useful to researchers: expression, variation, comparative genomics, and many more. The data can be accessed with simple text or sequence searches, or probed in depth with customized queries.


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