UCSC Genome Bioinformatics
  Frequently Asked Questions: Custom Annotation Tracks
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  Displaying personal annotation data in the Genome Browser
 

Question:
"How do I display my own personal annotation data in the Genome Browser?"

Response:
To create an annotation track that will display on the Genome Browser, you must first organize your data into one of the formats 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, 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.



  Adding a personal annotation track to the Genome Browser website
 

Question:
"I have an annotation track that I think might be of general interest to the research community. Will UCSC consider including my track in their browser?"

Response:
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 genome@soe.ucsc.edu. 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.



  Defining filter parameters for custom tracks
 

Question:
"Is it possible to define a filter parameter for a custom track to highlight certain features?"

Response:
This feature is not currently implemented.



  Coloring a custom track using the useScore parameter
 

Question:
"When designing a custom track, is there a way to assign specific colors to each segment, as is done in the mouse/rat synteny tracks? Is there a way to assign a value range for the useScore variable such that I can have four shades and specify the value range for each?"

Response:
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.



  Constructing a Genome Browser URL
 

Question:
"How can I construct a URL to retrieve data from the Genome Browser? What do the various parameters in the Genome Browser URLs mean?"

Response:
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.



  Using the hgsid parameter in a URL
 

Question:
"Should I use the hgsid parameter in my URL?"

Response:
Avoid using hgsid -- it is a temporary identifier, and will typically stop working after a day.



  Creating a details page for a custom annotation track
 

Question:
"While working on a custom track, we noticed that the feature details page for custom track looks different from regular tracks on the site. Is the details page for a custom track customizable?"

Response:
"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."



  Custom annotation track troubleshooting
 

Question:
"When I click the Submit button, I get the error message "line # of custom input: BED chromStarts[i] must be in ascending order"."

Response:
We have tightened up the input checking on custom tracks. 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.



  Error 500: Internal server error
 

Question:
"I'm getting an Error 500 when trying to upload my custom track(s). What am I doing wrong?"

Response:
"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."



  Byte-range request error
 

Question:
"When I try to visualize my custom track, I receive the error 'Byte-range request was ignored by server.'"

Response:
"This error occurs when a web server is not configured properly or does not support byte-ranges. Click here for more information."



  Error when using BedToBigBed or other utilities because of header track lines
 

Question:
"Why does my custom track fail when I use bedToBigBed or utilities like validateFiles?"

Response:
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 "track type=..." line that is specific for loading the data in the Browser. This line will cause raw data files to fail validation by other tools, such as bedToBigBed or 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.