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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

Leibovich Limor et al., Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs. Algorithms for Molecular Biology (2014) doi:10.1186/1748-7188-9-11

Konstantoulas James Constantine et al., Mouse mammary tumor virus-based vector transduces non-dividing cells, enters the nucleus via a TNPO3-independent pathway and integrates in a less biased fashion than other retroviruses. Retrovirology (2014) doi:10.1186/1742-4690-11-34

Zhu Ying et al., XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons Comparative and evolutionary genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-343

Ren Fang et al., Identification of differentially methylated genes in the malignant transformation of ovarian endometriosis. Journal of Ovarian Research (2014) doi:10.1186/1757-2215-7-73

Cui Xiaobin et al., Inactivation of miR-34a by aberrant CpG methylation in Kazakh patients with esophageal carcinoma. Journal of Experimental Clinical Cancer Research (2014) doi:10.1186/1756-9966-33-20

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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