Learn about the Browser: Difference between revisions

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== Statistics, overviews ==
== Statistics, overviews ==
*[[Gene_Set_Summary_Statistics]]
*[[Gene_Set_Summary_Statistics]]
* [http://genome-test.cse.ucsc.edu/~hiram/WEBStats/ Web hit statistics of the UCSC browser] (does anyone know if Ensembl is publishing their webhits?)
* [http://genome-test.cse.ucsc.edu/~hiram/WEBStats/ Web hit statistics of the UCSC browser]  


[[Category:Technical FAQ]]
[[Category:Technical FAQ]]

Revision as of 16:58, 25 February 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

Statistics, overviews