Learn about the Browser: Difference between revisions

From genomewiki
Jump to navigationJump to search
No edit summary
Line 83: Line 83:
== Developing with the UCSC API ==
== Developing with the UCSC API ==
* [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-March/001677.html Debug the cgi-scripts with GDB]
* [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-March/001677.html Debug the cgi-scripts with GDB]
* Understand the [http://biostar.stackexchange.com/questions/3669/is-there-such-a-thing-as-a-ucsc-api/3723#3723 binning scheme]


== Statistics, overviews ==
== Statistics, overviews ==

Revision as of 23:51, 29 January 2011

This page links to various pages that will help you to learn more about the UCSC Genome Browser. It 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