Learn about the Browser: Difference between revisions
From genomewiki
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 10: | Line 10: | ||
** Look at the [http://genome-test.cse.ucsc.edu/eng/ old documentation website with lots of developer documentation] | ** Look at the [http://genome-test.cse.ucsc.edu/eng/ old documentation website with lots of developer documentation] | ||
** [http://genome.ucsc.edu/admin/mirror.html Mirror the browser on your (linux) machine], search through the [http://genome.ucsc.edu/mirror.html mailing list] when you have problems and read the documentation in the directory [http://www.cse.ucsc.edu/~kent/src/unzipped/product/ kent/src/product] (hey, why do they lock the handy "unzipped" folder ?) | ** [http://genome.ucsc.edu/admin/mirror.html Mirror the browser on your (linux) machine], search through the [http://genome.ucsc.edu/mirror.html mailing list] when you have problems and read the documentation in the directory [http://www.cse.ucsc.edu/~kent/src/unzipped/product/ kent/src/product] (hey, why do they lock the handy "unzipped" folder ?) | ||
*** [http://bergman-lab.blogspot.com/2009/03/compiling-ucsc-source-tree-utilities-on.html some hints for MacOS users] | |||
** Try to get an impression how the original annotations were created (well, I said, "try"...) , in the [http://www.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/ 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 | ** Try to get an impression how the original annotations were created (well, I said, "try"...) , in the [http://www.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/ 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 | ||
** [http://genome.ucsc.edu/admin/jk-install.html Install the source tree] ([[the source tree|What's this?]]), compile it (comment out the -Wall in src/inc/common.mk) 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. :) | ** [http://genome.ucsc.edu/admin/jk-install.html Install the source tree] ([[the source tree|What's this?]]), compile it (comment out the -Wall in src/inc/common.mk) 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. :) | ||
Revision as of 10:33, 14 October 2009
Documentation is still somewhat dispersed. Here are some starting points:
- Using the browser website:
- 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 on your own Unix machine:
- 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
