Learn about the Browser: Difference between revisions

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* 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"]
* 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]
* 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 11:35, 8 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