Learn about the Browser: Difference between revisions

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== Download the data of the genome browser (sequences and annotations) ==
== Download the data of the genome browser (sequences and annotations) ==
* Be aware that internal coordinates (not website) are [[Coordinate_Transforms|0-based]]!
* Be aware that internal coordinates (not those shown on the website) are [[Coordinate_Transforms|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)
* 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):
* Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):

Revision as of 11:18, 6 January 2011

This list 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

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