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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

Paci Paola et al., Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer Systems physiology, pharmacology and medicine. BMC Systems Biology (2014) doi:10.1186/1752-0509-8-83

Xie Lan et al., MKL1/2 and ELK4 co-regulate distinct serum response factor (SRF) transcription programs in macrophages Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-301

Chilamakuri Reddy Chandra Sekhar et al., Performance comparison of four exome capture systems for deep sequencing Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-449

Mascelli Samantha et al., Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord. Molecular Cytogenetics (2014) doi:10.1186/1755-8166-7-31

Shen Li et al., ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases Transcriptomic methods. BMC Genomics (2014) doi:10.1186/1471-2164-15-284

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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