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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

Li Wentian et al., Diminishing return for increased Mappability with longer sequencing reads: implications of the k -mer distributions in the human genome Sequence analysis (methods). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-2

Stueve Ryan Theresa et al., CYP19A1 promoter methylation in saliva associated with milestones of pubertal timing in urban girls Genetics and congenital disorders. BMC Pediatrics (2014) doi:10.1186/1471-2431-14-78

Whelehan J Cormac et al., Characterisation and expression profile of the bovine cathelicidin gene repertoire in mammary tissue Non-human and non-rodent vertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-128

von der Heyde Silvia et al., Dynamics of mRNA and polysomal abundance in early 3T3-L1 adipogenesis Transcriptomic methods. BMC Genomics (2014) doi:10.1186/1471-2164-15-381

Frietze Seth et al., Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-520

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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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
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