Learn about the Browser: Difference between revisions
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* Using the browser: | * Using the browser: | ||
** Follow the video tutorials and browse through the slides made by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]. | ** Follow the video tutorials and browse through the slides made by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]. | ||
** | ** Browse over the basic materials written by the gurus themselves: The [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html User's guide] and the [http://genome.ucsc.edu/FAQ/ FAQs]. An additional page with link similar to this one is also called [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 the many [http://genome.ucsc.edu/FAQ/FAQformat.html different formats] | ** Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in the many [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]. Try not to ask too silly questions, you'll regret it one day, as they might appear as the first hit when someone is searching for your name on google... (At least I do. --Max :-) ) | ** Subscribe to the [http://www.soe.ucsc.edu/mailman/listinfo/genome mailing list] or [http://genome.ucsc.edu/contacts.html search through it]. Try not to ask too silly questions, you'll regret it one day, as they might appear as the first hit when someone is searching for your name on google... (At least I do. --Max :-) ) | ||
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** 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 kent/src/product/README.trackDb) and [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation] about this | ** 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 kent/src/product/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-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 | ** [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]] | ** 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]] | ||
[[Category:Technical FAQ]] | [[Category:Technical FAQ]] | ||
Revision as of 10:30, 14 October 2009
Documentation is somewhat dispersed, now let's see where we can learn something about this thing...
- Using the browser:
- Follow the video tutorials and browse through the slides made by Openhelix.
- Browse over the basic materials written by the gurus themselves: The User's guide and the FAQs. An additional page with link similar to this one is also called "Learning about the browser"
- Type in (manually) a couple of custom tracks in the many different formats
- Subscribe to the mailing list or search through it. Try not to ask too silly questions, you'll regret it one day, as they might appear as the first hit when someone is searching for your name on google... (At least I do. --Max :-) )
- Installling the browser locally:
- Look at the old documentation website with lots of developer documentation
- Mirror the browser on your (linux) machine, search through the mailing list when you have problems and read the documentation in the directory kent/src/product (hey, why do they lock the handy "unzipped" folder ?)
- Try to get an impression how the original annotations were created (well, I said, "try"...) , in the makeDb-files (make sure you also read kent/src/hg/makeDb/bashVsCsh is you're not a guru yet) and create your own annotations as textfiles
- Install the source tree (What's this?), compile it (comment out the -Wall in src/inc/common.mk) 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 kent/src/product/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
