Learn about the Browser: Difference between revisions
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== Use the browser website == | == Use the browser website == | ||
* Video tutorials and slides by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix] | |||
* Basic materials written by the gurus: The [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html User's guide] and the [http://genome.ucsc.edu/FAQ/ FAQs]. | |||
* A similar page to this one [http://genome-test.cse.ucsc.edu/eng/ "Learning about the browser"] | |||
* Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in [http://genome.ucsc.edu/FAQ/FAQformat.html different formats] | |||
* Subscribe to the [http://www.soe.ucsc.edu/mailman/listinfo/genome mailing list] or [http://genome.ucsc.edu/contacts.html 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 (SQL and files) and process them on your machine == | == Access the data of the genome browser (SQL and files) and process them on your machine == | ||
* Be aware that internal coordinates (not website) are [[Coordinate_Transforms|0-based]]! | |||
* SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]): | |||
** [http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Public mysql access] | |||
** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [http://genomewiki.ucsc.edu/images/1/1a/ISMB2008_UCSC.ppt Example session] | |||
** [http://genomewiki.cse.ucsc.edu/index.php/Image:Kent_allJoiner.ppt The all.joiner file], describes relations between all database tables | |||
* Flat-file data (in /gbdb and on the [http://genome.ucsc.edu/FAQ/FAQdownloads#download1 ftp server]) | |||
** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats] | |||
== 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] | |||
* On a linux machine: [http://genome.ucsc.edu/admin/jk-install.html Compile the browser source code] (make sure you get those [[Build_Environment_Variables|environment variables right]] or [http://genome.ucsc.edu/admin/mirror.html mirror a complete browser]. 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://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] | |||
** [[Browser_Mirrors|Updating it automatically]] | |||
* Try to get an impression how the original annotations were created (well, I said, "try"...) , in the [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/ makeDb-files] (make sure you also read [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh] is you're not a guru yet) and create your own annotations as textfiles | |||
* [http://genome.ucsc.edu/admin/jk-install.html Install the source tree] ([[the source tree|What's this?]]), compile it (see also: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]) and play with its tools, [http://genome.ucsc.edu/contacts.html searching through the archives] or this [[:Category:Technical FAQ| 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 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 [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb README.trackDb]) and [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation] about this | |||
* [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] | |||
* If you will still have problems from time to time with the process of blatting/blastzing/chaining/netting, refer to [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]] | |||
== Statistics, overviews == | == Statistics, overviews == | ||
Revision as of 10:53, 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 (SQL and files) and process them on your machine
- Be aware that internal coordinates (not website) are 0-based!
- SQL-stored data (FAQ):
- Public mysql access
- Table Browser, Example session
- The all.joiner file, describes relations between all database tables
- 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
- 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
- Try to get an impression how the original annotations were created (well, I said, "try"...) , in the makeDb-files (make sure you also read bashVsCsh is you're not a guru yet) and create your own annotations as textfiles
- 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 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
- If you will still have problems from time to time with the process of blatting/blastzing/chaining/netting, refer to Angies mental model and Max's howto
