Learn about the Browser: Difference between revisions
From genomewiki
Jump to navigationJump to search
| Line 10: | Line 10: | ||
== Access the data of the genome browser and process them on your machine == | == Access the data of the genome browser and process them on your machine == | ||
* Be aware that internal coordinates (not website) are [[Coordinate_Transforms|0-based]]! | * Be aware that internal coordinates (not website) are [[Coordinate_Transforms|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: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles): | ||
** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [http://genomewiki.ucsc.edu/images/1/1a/ISMB2008_UCSC.ppt Example session] | ** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [http://genomewiki.ucsc.edu/images/1/1a/ISMB2008_UCSC.ppt Example session] | ||
* SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]): | * SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]): | ||
| Line 16: | Line 16: | ||
** [http://genomewiki.cse.ucsc.edu/index.php/Image:Kent_allJoiner.ppt The all.joiner file], describes relations between all database tables | ** [http://genomewiki.cse.ucsc.edu/index.php/Image:Kent_allJoiner.ppt The all.joiner file], describes relations between all database tables | ||
** For all genes-related tables, there is a [http://genome-test.cse.ucsc.edu/images/knownGeneSchema.gif graphical map] (sub-optimal layout :-) | ** For all genes-related tables, there is a [http://genome-test.cse.ucsc.edu/images/knownGeneSchema.gif graphical map] (sub-optimal layout :-) | ||
* Flat-file data | * Flat-file data: Download from the [http://genome.ucsc.edu/FAQ/FAQdownloads#download1 ftp server] (stored in /gbdb on browser servers) | ||
** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats] | ** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats] | ||
Revision as of 16:25, 5 December 2009
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!
- 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):
- 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)
Installling the browser locally on your own Unix machine and extend it
- 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
- Add tracks to your own mirror:
- Charles Sugnet's presentation about TrackDB
- 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
- Sequence your genome of interest and create a browser for it
- Whole-genome alignment pipeline: Angies mental model and Max's howto
- How the UCSC folks created their tracks:
- UCSC's makeDb-files
- Some explanations how to read their files: bashVsCsh
- The source tree:
- 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
- some hints for MacOS users
- 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
Statistics, overviews
- Gene_Set_Summary_Statistics
- Web hit statistics of the UCSC browser (does anyone know if Ensembl is publishing their webhits?)
