Learn about the Browser: Difference between revisions
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== Installling the browser locally on your own Unix machine and extend it == | == Installling the browser locally on your own Unix machine and extend it == | ||
* The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation] | * The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation] | ||
* | * Create a mirror of the UCSC site: | ||
** [http://genome.ucsc.edu/admin/mirror.html mirror a complete browser]. | ** [http://genome.ucsc.edu/admin/mirror.html mirror a complete browser]. | ||
** [[Browser_Mirrors|Updating the data automatically from UCSC]] | ** [[Browser_Mirrors|Updating the data automatically from UCSC]] | ||
* | * Add tracks to your own mirror: | ||
** [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation about TrackDB] | ** [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation about TrackDB] | ||
** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb The structure of the trackDB] | ** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb The structure of the trackDB] | ||
** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ The trackDB statements] | ** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ The trackDB statements] | ||
* How UCSC folks created their tracks: | ** 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/admin/ a similar place with hgSearchSpec docs and statistics (the system to search for ids)] can be found completely off-track | |||
** [http://genome.ucsc.edu/FAQ/FAQlicense#license4 Sequence your genome of interest and create a browser for it] | |||
** Whole-genome alignment pipeline: [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]] | |||
* How the UCSC folks created their tracks: | |||
** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/ UCSC's makeDb-files] | ** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/ UCSC's makeDb-files] | ||
** Some explanations how to read their files: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh] | ** Some explanations how to read their files: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh] | ||
* [http://genome | * The source tree: | ||
* [http:// | ** What is the [[the source tree]] ? | ||
* | ** What is available in the [[Kent source utilities]] ? | ||
** [http://genome.ucsc.edu/admin/jk-install.html Compile the browser source code] | |||
** make sure you get those [[Build_Environment_Variables|environment variables right]] | |||
** [http://bergman-lab.blogspot.com/2009/03/compiling-ucsc-source-tree-utilities-on.html some hints for MacOS users] | |||
** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source] | |||
** [http://genome.ucsc.edu/contacts.html searching through the archives] or the [[:Category:Technical FAQ| Technical-FAQ-Category of the wiki]] when you have problems | |||
== Statistics, overviews == | == Statistics, overviews == | ||
Revision as of 11:16, 2 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!
- 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 (in /gbdb and on the ftp server)
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:
- 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?)
