Learn about the Browser: Difference between revisions

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*** Examples for the composite statements in trackDb, from the [Encode trackDb http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra]
*** Examples for the composite statements in trackDb, from the [Encode trackDb http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra]
* When you run into problems, search through the [http://genome.ucsc.edu/mirror.html mailing list] when you have problems and read the documentation in the directory [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/ kent/src/product]
* When you run into problems, search through the [http://genome.ucsc.edu/mirror.html mailing list] when you have problems and read the documentation in the directory [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/ kent/src/product]
** [http://genome-test.cse.ucsc.edu/~hiram/rgbItemExamples.html|RGB color codes]
** [http://genome-test.cse.ucsc.edu/~hiram/rgbItemExamples.html#RGB color codes]
** [http://genome-test.cse.ucsc.edu/admin/ a similar place with hgSearchSpec docs and statistics (the system to search for ids)] can be found completely off-track
** [http://genome-test.cse.ucsc.edu/admin/ a similar place with hgSearchSpec docs and statistics (the system to search for ids)] can be found completely off-track
* Create a browser for a [[Building a new genome database|completely new genome]]
* Create a browser for a [[Building a new genome database|completely new genome]]

Revision as of 21:50, 19 January 2018

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

  • Bob Kuhn is giving workshops throughout the year at several US conferences, in Europe, Australia and Asia
  • Video tutorials and slides by Openhelix
  • An introduction on Nature Education
  • Basic materials written by the gurus: The User's guide and the FAQs.
  • View a gallery of browser sessions that highlight interesting data sets.
  • Type in (manually) a couple of custom tracks in different formats (just try bed for a start, you mostly won't need the others)
  • Subscribe to the mailing list or search through it. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.

Download the data of the genome browser (sequences and annotations)

  • Be aware that internal coordinates (not those shown on the website) are 0-based! (only exception: wiggle)
  • 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