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
• On a linux machine: Compile the browser source code (make sure you get those environment variables right or 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 it automatically
• 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. :)
• How to create genome browser annotation tracks: makeDb-files (also read bashVsCsh if you're not a Unix guru yet) and create your own annotations as textfiles
• Load them onto the browser: Read Jim's Documentation how to add your own tracks to your own browser (by modifying a trackDb.ra-file, documented in kent/src/hg/makeDb/addTrack.doc and README.trackDb) and Charles Sugnet's presentation about this
• 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