Learn about the Browser: Difference between revisions

From genomewiki
Jump to navigationJump to search
Line 41: Line 41:
** Whole-genome alignment pipeline: [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]]
** Whole-genome alignment pipeline: [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]]


== Compiling the source tree ==
== Compile the source tree to get your own genomics pipeline started ==
** What is the [[the source tree]] ?
** What is the [[the source tree]] ?
** What is available in the [[Kent source utilities]] ?
** What is available in the [[Kent source utilities]] ?

Revision as of 09:52, 8 December 2009

Documentation is still somewhat dispersed. Here are some starting points:

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

The details behind the UCSC genome browser (making of)

Statistics, overviews