- Genome Browser
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To create an annotation track that will display on the Genome Browser, you must first organize your data into a format supported by the browser custom track feature: GTF, GFF, BED, WIG, or PSL. Then, upload your data into the Genome Browser on the Add Custom Tracks page. Once you've created your annotation track, you can share it with others over the internet by putting your annotation file on your website and then creating a custom URL that allows others to directly start the browser with your track displayed.
Read the Creating custom annotation tracks section in the Genome Browser User's Guide for a step-by-step description of how to format and display a custom annotation track and create a custom URL.
We are always interested in receiving new annotation tracks for the Genome Browser, and encourage our users to share their tracks with us and others in the research community. Please send the URL for your track -- along with a description of the methods, data, and format used -- to firstname.lastname@example.org. If we determine that your track is of sufficient general interest to distribute as part of our browser, we'll work with you to include it.
In addition to the standard set of tracks displayed on the Genome Browser page, we also have a Custom Annotation Tracks page that contains contributed tracks we are unable to display in the main browser (for example, tracks that are of too specific an interest or are too sparse). We welcome contributions to this page.
This feature is not currently implemented.
Currently useScore works only with tracks that are black or specific shades of brown or blue. The score range is 0-1000. To display four shades, use the scores 0, 333, 666, and 1000.
One way to determine how to construct a correct URL is to open a Genome Browser link in which you are interested and examine how the Genome Browser constructs the URL. See the User's Guide for a discussion of the basic components of a Genome Browser URL. Note that the c parameter that appears in some URLs specifies the chromosome name or the chromosome name and position.
Avoid using hgsid -- it is a temporary identifier, and will typically stop working after a day.
You can add a link from a details page to an external web page containing additional information about the feature by using the track line url attribute. In the annotation file, set the url attribute in the track line to point to a publicly available page on a web server. The url attribute substitutes each occurrence of '$$' in the URL string with the name defined by the name attribute. You can take advantage of this feature to provide individualized information for each feature in your track by creating HTML anchors that correspond to the feature names in your web page.
This error is caused by a logical conflict in the Genome Browser software. It accepts custom GFF tracks that have multiple "exons" at the same position, but not BED tracks that have this feature. Because the browser translates GFF tracks to BED format before storing the custom track data, GFF tracks with multiple exons will cause an error when the BED is read back in. To work around this problem, remove duplicate lines in the GFF track.
This error may occur when trying to upload a file that is too large. For larger data sets, we suggest using bigBed and bigWig file formats. More information about selecting a format can be found here.
This error occurs when a web server is not configured properly or does not support byte-ranges. Click here for more information.
bedToBigBedor utilities like
These utilities can fail when the input includes custom-track-specific lines at the top of the file
that are not considered part of the data. Many of the custom track examples on the
File Format page include a "
type=..." line that is specific for loading the data into the Browser. This line will
cause raw data files to fail validation by other tools, such as
validateFiles, outside of the Browser. To see an example of using
bedToBigBed with correct input data types, follow this
link. More information about track
lines can be found here.