Learn about the Browser: Difference between revisions

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* 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):
** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [http://genomewiki.ucsc.edu/images/1/1a/ISMB2008_UCSC.ppt Example session]
** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [[Image:ISMB2008_UCSC.ppt|Example session]]
* SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]):
* SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]):
** [http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Public mysql access]
** [http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Public mysql access]
** [http://genomewiki.cse.ucsc.edu/index.php/Image:Kent_allJoiner.ppt The all.joiner file], describes relations between all database tables
** [[Image:Kent_allJoiner.ppt|The all.joiner file]], describes relations between all database tables
** For all genes-related tables, there is a [http://genome-test.cse.ucsc.edu/images/knownGeneSchema.gif graphical map] (sub-optimal layout :-)
** For all genes-related tables, there is a [http://genome-test.cse.ucsc.edu/images/knownGeneSchema.gif graphical map] (sub-optimal layout :-)
* Flat-file data: Download from the [http://genome.ucsc.edu/FAQ/FAQdownloads#download1 ftp server] (stored in /gbdb on browser servers)
* Flat-file data: Download from the [http://genome.ucsc.edu/FAQ/FAQdownloads#download1 ftp server] (stored in /gbdb on browser servers)

Revision as of 00:53, 4 December 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