Learn about the Browser: Difference between revisions

From genomewiki
Jump to navigationJump to search
No edit summary
Line 73: Line 73:
* [http://genome.ucsc.edu/FAQ/FAQlicense#license4 How to create a browser for a new genome from scratch]
* [http://genome.ucsc.edu/FAQ/FAQlicense#license4 How to create a browser for a new genome from scratch]
* [http://users.soe.ucsc.edu/~markd/genbank-update/ Genbank Updates]
* [http://users.soe.ucsc.edu/~markd/genbank-update/ Genbank Updates]
== Developing with the UCSC API ==
* [[Debugging cgi-scripts]]


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

Revision as of 10:00, 24 March 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