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!
• 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, 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: Download from the ftp server (stored in /gbdb on browser servers)
  • Text file formats

Install a copy of the browser on your own machine (Unix or Mac)

• The old documentation website with developer documentation
• Create a mirror of the UCSC site:
  • mirror a complete browser
  • Almost the same document, but on the wiki, some more info
  • Updating the data automatically from UCSC
  • Pro and cons of storing custom tracks in MySQL or as flat files
  • How are cookies handled by the browser?
  • Any news if the browser compiles on Windows (Cygwin) ?

Modify your own copy of the browser

• Add tracks to your own mirror:
  • Charles Sugnet's presentation about TrackDB
  • How_to_add_a_track_to_a_mirror
  • The structure of the trackDB
  • The trackDB statements
  • When you run into problems, search through the mailing list when you have problems and read the documentation in the directory kent/src/product
  • a similar place with hgSearchSpec docs and statistics (the system to search for ids) can be found completely off-track

Compile the source tree to get your own genomics pipeline started

• • What is the the source tree ?
  • What is available in the Kent source utilities ?
  • Compile the browser source code
  • make sure you get those environment variables right
  • Walkthroughs for...
    • MacOS X users
    • Debian and Ubuntu
  • See also the textfile README.building.source README.building.source
  • searching through the archives or the Technical-FAQ-Category of the wiki when you have problems

Making Of: How the UCSC genome annotations are created

• How the UCSC folks created their tracks:
  • UCSC's makeDb-files
  • Some explanations how to read the makeDb files: bashVsCsh
  • Notes on the history of the internal tools: Autosql. Blastz. Chains and nets
• Whole-genome multiple alignments (Chains_Nets)
  • Mm9_multiple_alignment
  • Whole-genome alignment pipeline: Angies mental model and Max's howto
  • How to create a browser for a new genome from scratch

Statistics, overviews

• Gene_Set_Summary_Statistics
• Web hit statistics of the UCSC browser (does anyone know if Ensembl is publishing their webhits?)