Learn about the Browser

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

Use the browser website

• Video tutorials and slides by Openhelix
• Basic materials written by the gurus: The User's guide and the FAQs.
• A similar page to this one "Learning about the browser"
• Type in (manually) a couple of custom tracks in different formats
• 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.

Access the data of the genome browser and process them on your machine

• Be aware that internal coordinates (not website) are 0-based!
• The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):
  • Table Browser, Example session
• SQL-stored data (FAQ):
  • Public mysql access
  • The all.joiner file, describes relations between all database tables
  • For all genes-related tables, there is a graphical map (sub-optimal layout :-)
• Flat-file data (in /gbdb and on the ftp server)
  • Text file formats

Installling the browser locally on your own Unix machine and extend it

• The old documentation website with developer documentation
• Compile Code/Install Data:
  • Compile the browser source code
  • make sure you get those environment variables right
  • mirror a complete browser.
  • When you run into problems, search through the mailing list when you have problems and read the documentation in the directory kent/src/product
  • some hints for MacOS users
  • See also the textfile README.building.source README.building.source
  • Updating the data automatically from UCSC
• Install the source tree (What's this?), compile it (see also: README.building.source) and play with its tools, searching through the archives or this wiki when you have problems, or browse the list of Kent source utilities available on this wiki. Don't expect to understand what is available, it's not possible to remember them anyways. :)
• Load tracks into your browser:
  • Charles Sugnet's presentation about TrackDB
  • The structure of the trackDB
  • The trackDB statements
• How UCSC folks created their tracks:
  • UCSC's makeDb-files
  • Some explanations how to read their files: bashVsCsh

• a similar place with hgSearchSpec docs and statistics (the system to search for ids) can be found completely off-track
• Sequence your genome of interest and create a browser for it
• Whole-genome alignment pipeline: Angies mental model and Max's howto

Statistics, overviews

• • Gene_Set_Summary_Statistics