Learn about the Browser: Difference between revisions

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== Use the browser website ==
== Use the browser website ==
* Bob Kuhn is giving workshops throughout the year in 2011 at several US conferences and in Europe (Madrid, Barcelona, Manchester, London, Amsterdam). Email him for details.
* Video tutorials and slides by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]
* Video tutorials and slides by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]
* Basic materials written by the gurus: The [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html User's guide] and the [http://genome.ucsc.edu/FAQ/ FAQs].  
* Basic materials written by the gurus: The [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html User's guide] and the [http://genome.ucsc.edu/FAQ/ FAQs].  
* A similar page to this one [http://genome-test.cse.ucsc.edu/eng/ "Learning about the browser"]
* A similar page to this one [http://genome-test.cse.ucsc.edu/eng/ "Learning about the browser"]
* View a [[Genome_Browser_Session_Gallery|gallery]] of browser sessions that highlight interesting data sets.
* View a [[Genome_Browser_Session_Gallery|gallery]] of browser sessions that highlight interesting data sets.
* Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in [http://genome.ucsc.edu/FAQ/FAQformat.html different formats]
* Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in [http://genome.ucsc.edu/FAQ/FAQformat.html different formats] (just try bed for a start, you mostly won't need the others)
* If you need to graph data, there are [[Selecting_a_graphing_track_data_format|different graphing formats]]
** Try typing "chr1 1 1000 Hello_World!" as a custom track
** If you need to graph data, there are [[Selecting_a_graphing_track_data_format|different graphing formats]]
* Subscribe to the [http://www.soe.ucsc.edu/mailman/listinfo/genome mailing list] or [http://genome.ucsc.edu/contacts.html search through it]. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.
* Subscribe to the [http://www.soe.ucsc.edu/mailman/listinfo/genome mailing list] or [http://genome.ucsc.edu/contacts.html search through it]. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.



Revision as of 23:57, 29 January 2011

This page links to various pages that will help you to learn more about the UCSC Genome Browser. It is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones administrator access to a Linux webserver.

Use the browser website

  • Bob Kuhn is giving workshops throughout the year in 2011 at several US conferences and in Europe (Madrid, Barcelona, Manchester, London, Amsterdam). Email him for details.
  • Video tutorials and slides by Openhelix
  • Basic materials written by the gurus: The User's guide and the FAQs.
  • A similar page to this one "Learning about the browser"
  • View a gallery of browser sessions that highlight interesting data sets.
  • Type in (manually) a couple of custom tracks in different formats (just try bed for a start, you mostly won't need the others)
  • Subscribe to the mailing list or search through it. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.

Download the data of the genome browser (sequences and annotations)

  • Be aware that internal coordinates (not those shown on the website) are 0-based!
  • Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)
  • Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):
  • SQL-stored data (FAQ):
  • Flat-file data: Download from the ftp server (stored in /gbdb on browser servers)

Install a copy of the browser on your own machine (Unix or Mac)

Compile the UCSC source tree and analyze genomes yourself

Modify your own copy of the browser

Making Of: How the UCSC genome annotations are created

Developing with the UCSC API

Statistics, overviews