Learn about the Browser: Difference between revisions

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*** [[Source tree compilation on Debian/Ubuntu|Debian and Ubuntu]]
*** [[Source tree compilation on Debian/Ubuntu|Debian and Ubuntu]]
*** [[CentOS Notes]]
*** [[CentOS Notes]]
*** Windows: see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html] but your mileage may vary to get everything to compile.
** The most common problem on the mailing list are harmless warnings that trigger errors. To ignore these, which is usually safe, [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2006-November/000251.html remove the -Wall option from the makefile]
** The most common problem on the mailing list are harmless warnings that trigger errors. To ignore these, which is usually safe, [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2006-November/000251.html remove the -Wall option from the makefile]
** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]
** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]

Revision as of 10:55, 20 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

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, Windows optional)

Analyze UCSC genome data files on your own machine

Modify your own copy of the browser


Making Of: How the UCSC genome annotations are created

Statistics, overviews