Learn about the Browser: Difference between revisions

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Documentation is still somewhat dispersed. Here are some starting points:
This page links to various pages that will help you to learn more about the UCSC Genome Browser. It is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones administrator access to a Linux webserver.


* Using the browser website:
== Use the browser website ==
** Video tutorials and slides by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]
* Bob Kuhn is giving workshops throughout the year at several US conferences, in Europe, Australia and Asia
** 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].  
** Read about how to [http://genome.ucsc.edu/training/ | host]
** A similar page to this one [http://genome-test.cse.ucsc.edu/eng/ "Learning about the browser"]
* Video tutorials and slides by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]
** Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in [http://genome.ucsc.edu/FAQ/FAQformat.html different formats]
* An introduction on [http://www.nature.com/scitable/ebooks/guide-to-the-ucsc-genome-browser-16569863/contents Nature Education]
** 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.
* 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].  
* View a [http://genome.ucsc.edu/cgi-bin/hgPublicSessions gallery] of browser sessions that highlight interesting data sets.
* Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in [http://genome.ucsc.edu/FAQ/FAQformat.html different formats] (just try bed for a start, you mostly won't need the others)
** Try typing "chr1 1 1000 Hello_World!" as a custom track
** If you need to graph data, there are [[Selecting_a_graphing_track_data_format|different graphing 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.


* Accessing the data of the genome browser (SQL and files):
== Download the data of the genome browser (sequences and annotations) ==
** SQL-stored data:
* Be aware that internal coordinates (not those shown on the website) are [[Coordinate_Transforms|0-based]]! (only exception: wiggle)
*** [http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Public mysql access]
* Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)
*** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [http://genomewiki.ucsc.edu/images/1/1a/ISMB2008_UCSC.ppt Example session]
* Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):
*** [http://genomewiki.cse.ucsc.edu/index.php/Image:Kent_allJoiner.ppt The all.joiner file], describes relations between all database tables
** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [[Image:ISMB2008_UCSC.ppt|Example session]]
** Flat-file data (in /gbdb and on the ftp server)
* SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]):
*** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats]
** [http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Public mysql access]
** [[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.soe.ucsc.edu/images/knownGeneSchema.gif graphical map] (sub-optimal layout :-)
* 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]


* Installling the browser locally on your own Unix machine:
== Install a copy of the browser on your own machine (Unix or Mac) ==
** The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation] 
* Create a mirror of the UCSC site:
** 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://genome.ucsc.edu/admin/mirror.html Official FAQ: mirror a complete browser], the main reference for browser installation
*** [http://bergman-lab.blogspot.com/2009/03/compiling-ucsc-source-tree-utilities-on.html some hints for MacOS users]
** [[Browser_Installation|Inofficial FAQ: Browser Installation]], on the wiki, a lot more info
*** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]
** [[Minimal Browser Installation|Mirror only selected genomes]]
*** [[Browser_Mirrors|Updating it automatically]]
** Adapt your cgi-bin/[[Hg.conf]] file for your mirror
** 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
** Be prepared that you'll need to create at least and also download parts of the hg18. At least mouse genomes still depend on it.
** [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. :)
** Make sure that you keep your own tracks separate, read this before loading any local data: [[Local_tracks_at_mirror_sites|Local TrackDB table]]
** 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
** [[Browser_Mirrors|Updating the data automatically from UCSC]]
** [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
** [[Using_custom_track_database|Pro and cons of storing custom tracks in MySQL or as flat files]]
** [http://genome.ucsc.edu/FAQ/FAQlicense#license4 Sequence your genome of interest and create a browser for it]
** [[Cookie_Session|How are cookies handled by the browser?]]
** 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]]
** [[Category:Mirror_Site_FAQ|All other documents in this category]]
** The [http://genome-test.soe.ucsc.edu/eng/ old documentation website with developer documentation]
**[[Running your own gfServer]] (=BLAT server), needed in cases where you don't want or cannot use the UCSC BLAT servers.


*Statistics, overviews
== Compile the UCSC source tree and analyze genomes yourself ==
** [[Gene_Set_Summary_Statistics]]
* The '''source tree''' (aka Kent source) is the collection of all tools used at the UCSC browser group
* You could also call this an '''API''', as you can use these tools from your own programs
* General introduction to the [[the source tree]]
* What is documented to be available in the [[Kent source utilities]]
** ... and what is [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/sources really available] in the source tree?
* Some important tools are already compiled (even for windows!) [http://hgdownload.soe.ucsc.edu/admin/exe/ from here]
* [http://genome.ucsc.edu/admin/jk-install.html Compile all tools (includes the browser webserver)] yourself
** The best starting point is the main zipfile: http://hgdownload.soe.ucsc.edu/admin/jksrc.zip
** You need to set some [[Build_Environment_Variables|environment variables]] before you start the compilation
** Walkthroughs for...
*** [http://bergmanlab.smith.man.ac.uk/?p=32 MacOS X users]
*** [[Source tree compilation on Debian/Ubuntu|Debian and Ubuntu]]
*** [[CentOS Notes]]
*** Windows: see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html] but your mileage may vary to get everything to compile.
 
** The most common problem on the mailing list are harmless warnings that trigger errors. "cc1: warnings being treated as errors". To ignore them, which is usually safe, [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2006-November/000251.html remove the -Wall option from the makefile]
** See also the textfile README.building.source [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]
** [http://genome.ucsc.edu/contacts.html Search through the archives] or the [[:Category:Technical FAQ| Technical-FAQ-Category of the wiki]] when you have problems
** Send an email to the mailing list if you cannot find the answer yourself
** Some more sophisticated genome pipelines
*** Create your own [[Whole_genome_alignment_howto|whole-genome alignment]]
*** Create your own [[LiftOver_Howto|liftOver file]]
 
== Modify your own copy of the browser ==
* You load track data into your mirror
** with the hgLoadxxx utils (e.g. hgLoadBed)
** and show meta data (name, type, possible controls, etc) on the browser by editing a textfile called trackDb.ra
* TrackDB documentation:
** [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation about TrackDB]
** [[How_to_add_a_track_to_a_mirror]]
** [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/product/README.trackDb The structure of the trackDB]
** [http://hgwdev.osoe.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ Full TrackDB-Documentation: shows all possible trackDB statements]
*** Examples: [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/human/hg19/trackDb.ra UCSC trackDb for hg19]
*** Examples for the composite statements in trackDb, from the [Encode trackDb http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra]
* 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.soe.ucsc.edu/~kent/src/unzipped/product/ kent/src/product]
** [http://genome-test.soe.ucsc.edu/~hiram/rgbItemExamples.html#RGB color codes]
** [http://genome-test.soe.ucsc.edu/admin/ a similar place with hgSearchSpec docs and statistics (the system to search for ids)] can be found completely off-track
* Create a browser for a [[Building a new genome database|completely new genome]]
** Slides of a class on [https://banana-slug.soe.ucsc.edu/_media/lecture_notes:genomebrowsersetup.pdf Creating a browser for new bacterial genome]
* The most difficult part: [[Writing_a_new_track_type|Adding a completely new track type and visualisation code to the browser]]
 
== Making Of: How the UCSC genome annotations are created ==
* How the UCSC folks created their tracks:
** The [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/ UCSC's makeDb-files] are a log of all commands that are necessary to re-create all annotations for a particular genome. 
** Some explanations how to read the makeDb files: [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh]
** The [http://hgwdev.soe.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ trackDb-files] are the "track database" of the browser. They include all instructions on how annotations are displayed (e.g. the type of display, colors, settings, options, filenames, etc.)
** [[Implementation_Notes|Notes on the history of the internal tools: Autosql. Blastz. Chains and nets]]
* Whole-genome multiple alignments ([[Chains_Nets]])
** [[Mm9_multiple_alignment]]
** Whole-genome alignment pipeline: [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]]
* [http://genome.ucsc.edu/FAQ/FAQlicense#license4 How to create a browser for a new genome from scratch]
* [http://users.soe.ucsc.edu/~markd/genbank-update/ Genbank Updates]
* Cross-links to other databases
** Outlinks for genes are copied from uniProt. The whole uniProt update process is rather complicated, see [[UCSC_Genes_Staging_Process]]
 
== Developing with the UCSC API ==
* [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-March/001677.html Debug the cgi-scripts with GDB]
* Understand the [http://biostar.stackexchange.com/questions/3669/is-there-such-a-thing-as-a-ucsc-api/3723#3723 binning scheme]
 
== Statistics, overviews ==
*[[Gene_Set_Summary_Statistics]]
* [http://genome-test.soe.ucsc.edu/~hiram/WEBStats/ Web hit statistics of the UCSC browser]  


[[Category:Technical FAQ]]
[[Category:Technical FAQ]]

Latest revision as of 07:30, 1 September 2018

This page links to various pages that will help you to learn more about the UCSC Genome Browser. It is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones administrator access to a Linux webserver.

Use the browser website

  • Bob Kuhn is giving workshops throughout the year at several US conferences, in Europe, Australia and Asia
  • Video tutorials and slides by Openhelix
  • An introduction on Nature Education
  • Basic materials written by the gurus: The User's guide and the FAQs.
  • View a gallery of browser sessions that highlight interesting data sets.
  • Type in (manually) a couple of custom tracks in different formats (just try bed for a start, you mostly won't need the others)
  • 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.

Download the data of the genome browser (sequences and annotations)

  • Be aware that internal coordinates (not those shown on the website) are 0-based! (only exception: wiggle)
  • Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)
  • 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):
  • Flat-file data: Download from the ftp server (stored in /gbdb on browser servers)

Install a copy of the browser on your own machine (Unix or Mac)

Compile the UCSC source tree and analyze genomes yourself

Modify your own copy of the browser

Making Of: How the UCSC genome annotations are created

Developing with the UCSC API

Statistics, overviews

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