The Genome Browser provides dozens of aligned annotation tracks that have been computed at UCSC or have been provided by outside collaborators. In addition to these standard tracks, it is also possible for users to upload their own annotation data for temporary display in the browser. These custom annotation tracks are viewable only on the machine from which they were uploaded and are automatically discarded 48 hours after the last time they are accessed, unless they are saved in a Session. Optionally, users can make custom annotations viewable by others as well. For a more stable option for custom annotations, we suggest -using track hubs. A third, more technical, option is to operate a mirror. Custom tracks work well for quickly displaying data, while track hubs are +using track hubs. A third, more technical, option +is to operate a mirror. Custom tracks work well for quickly displaying data, while track hubs are more configurable and permanent.
Custom tracks are a wonderful tool for research scientists using the Genome Browser. Because space is limited in the Genome Browser track window, many excellent genome-wide tracks cannot be included in the standard set of tracks packaged with the browser. Other tracks of interest may be excluded from distribution because the annotation track data is too specific to be of general interest or can't be shared until journal publication. In the past, many individuals and labs contributed custom tracks to the Genome Browser website for use by others. To view a list of these custom annotation tracks, click here.
Track hubs are now the preferred approach for viewing and sharing data on the Browser. Labs,
consortia, and institutions submit their hubs to be listed as a Public Hub. Track hubs require remotely hosted data. They use binary index
files which allow the browser to quickly access only what is relevant for the current region being
viewed in the browser. See the track hub help
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Step 1. Put your formatted annotation file on your web site. Be sure that the file
permissions allow it to be read by others.
Step 2. Construct a URL that will link this annotation file to the Genome Browser.
The URL must contain 3 pieces of information specific to your annotation data:
org=human. To specify a particular genome assembly for an organism, use the
db parameter, db=database_name, where database_name is the UCSC
code for the genome assembly. For a list of these codes, see the Genome Browser
FAQ. Examples of this include:
db=hg16 (Human July 2003 assembly), db=mm6 (Mouse Mar. 2005 assembly).genome=database_name, which acts in the same manner as
+ the db parameter. Here is an example using the house mouse (Mus musculus, 129S1_SvImJ)
+ assembly hub:
+ http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txtposition=chr_position, where chr_position is a chromosome number, with
or without a set of coordinates. Examples of this include: position=chr22,
position=chr22:15916196-31832390.hgt.customText=URL, where URL points to the annotation file on your website.
An example of an annotation file URL is http://genome.ucsc.edu/goldenPath/help/test.bed.
You can add other optional parameters to the URL: (Note: Display may vary if you have conflicting