Learn about the Browser: Difference between revisions

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** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats]
** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats]


== 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, Windows optional) ==
* The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation]   
* The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation]   
* Create a mirror of the UCSC site:
* Create a mirror of the UCSC site:
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** [[Using_custom_track_database|Pro and cons of storing custom tracks in MySQL or as flat files]]
** [[Using_custom_track_database|Pro and cons of storing custom tracks in MySQL or as flat files]]
** [[Cookie_Session|How are cookies handled by the browser?]]
** [[Cookie_Session|How are cookies handled by the browser?]]
** It seems that you can also run a mirror on windows (see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html]) but your mileage may vary to get everything to compile.
** It seems that you can also run a mirror on windows (see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html]) but your mileage may vary to get everything to compile. If you have one running, please update this wiki.


== Modify your own copy of the browser ==
== Modify your own copy of the browser ==

Revision as of 21:25, 16 January 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

Access the data of the genome browser and process them on your machine

  • 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, Windows optional)

Modify your own copy of the browser

Compile the source tree to get your own genomics pipeline started

Making Of: How the UCSC genome annotations are created

Statistics, overviews