Learn about the Browser: Difference between revisions

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== Install a copy of the browser on your own machine (Unix or Mac) ==
== Install a copy of the browser on your own machine (Unix or Mac) ==
* See also the next section about source tree installation, as the source tree toolset includes all CGI scripts for the UCSC browser installation (but you don't need to compile it, binaries for mirrors are provided at http://genome.ucsc.edu/admin/mirror.html#step6)
* Create a mirror of the UCSC site:
* Create a mirror of the UCSC site:
** [http://genome.ucsc.edu/admin/mirror.html Official FAQ: mirror a complete browser], the main reference for browser installation
** [http://genome.ucsc.edu/admin/mirror.html Official FAQ: mirror a complete browser], the main reference for browser installation

Revision as of 09:53, 7 April 2010

This list is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones a Linux webserver.

Use the browser website

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

  • Be aware that internal coordinates (not 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