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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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Recent BioMed Central research articles citing this resource

Riccardo Federica et al., Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers Italian Society of Bioinformatics (BITS): Annual Meeting 2013: Genomics Tenth Annual Meeting of the Italian Society of Bioinformatics (BITS). BMC Genomics (2014) doi:10.1186/1471-2164-15-S3-S1

Suderman Matthew et al., Childhood abuse is associated with methylation of multiple loci in adult DNA Genomic epidemiology. BMC Medical Genomics (2014) doi:10.1186/1755-8794-7-13

Bailly-Bechet Marc et al., “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files. Mobile DNA (2014) doi:10.1186/1759-8753-5-13

Zhang Xiao-Ou et al., Species-specific alternative splicing leads to unique expression of sno-lncRNAs Transcriptomic methods. BMC Genomics (2014) doi:10.1186/1471-2164-15-287

Walters-Conte B Kathryn et al., The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms Genome evolution and evolutionary systems biology. BMC Evolutionary Biology (2014) doi:10.1186/1471-2148-14-137

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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