Learn about the Browser: Difference between revisions

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Documentation is still somewhat dispersed. Here are some starting points:
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 ==
== Use the browser website ==

Revision as of 18:37, 14 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)

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