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. Optionally, users can make custom annotations viewable by others as well. 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. Many individuals and labs have contributed custom tracks to the Genome Browser website for use by others. To view a list of these custom annotation tracks, click the Custom Tracks link on the Genome Browser home page. Custom annotation tracks are similar to standard tracks, but never become part of the MySQL genome database. Each track has its own controller and persists even when not displayed in the Genome Browser window, e.g. if the position changes to a range that no longer includes the track. Typically, custom annotation tracks are aligned under corresponding genomic sequence, but they can also be completely unrelated to the data. For example, a track can be displayed under a long sequence consisting of millions of Ns. Genome Browser annotation tracks are based on files in line-oriented format. Each line in the file defines a display characteristic for the track or defines a data item within the track. Annotation files contain three types of lines: browser lines, track lines, and data lines. Empty lines and those starting with "#" are ignored. To construct an annotation file and display it in the Genome Browser, follow these steps: Step 1. Format the data set Step 2. Define the Genome Browser display characteristics Step 3. Define the annotation track display characteristics Example 1: track name=coords description="Chromosome coordinates list" visibility=2 chr22 20100000 20100100 chr22 20100011 20100200 chr22 20100215 20100400 chr22 20100350 20100500 chr22 20100700 20100800 chr22 20100700 20100900 Click here to view this track in the Genome Browser. Example 2: track name=spacer description="Blue ticks every 10000 bases" color=0,0,255, chr22 20100000 20100001 chr22 20110000 20110001 chr22 20120000 20120001 track name=even description="Red ticks every 100 bases, skip 100" color=255,0,0 chr22 20100000 20100100 first chr22 20100200 20100300 second chr22 20100400 20100500 third Click here to view this track in the Genome Browser. Example 3: browser hide all track name="BED track" description="BED format custom track example" visibility=2 color=0,128,0 useScore=1 chr22 1000 5000 itemA 960 + 1100 4700 0 2 1567,1488, 0,2512 chr22 2000 7000 itemB 200 - 2200 6950 0 4 433,100,550,1500 0,500,2000,3500 Click here to view this track in the Genome Browser. Step 4. Display your annotation track in the Genome Browser On the Add Custom Tracks page, load the annotation track data or URL for your custom track into the upper text box and the track documentation (optional) into the lower text box, then click the Submit button. Tracks may be loaded by entering text, a URL, or a pathname on your local computer. For more information on these methods, as well as information on creating and adding track documentation, see Loading a Custom Track into the Genome Browser. If you encounter difficulties displaying your annotation, read the section Troubleshooting Annotation Display Problems. Step 5. (Optional) Add details pages for individual track features 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 '$$' in the URL string with the name defined by the name attribute. You can take advantage of this feature to provide individualized information for each feature in your track by creating HTML anchors that correspond to the feature names in your web page. Example 4: browser hide all track name=clones description="Clones" visibility=2 color=0,128,0 useScore=1 url="http://genome.ucsc.edu/goldenPath/help/clones.html#$$" chr22 10000000 10004000 cloneA 960 chr22 10002000 10006000 cloneB 200 chr22 10005000 10009000 cloneC 700 chr22 10006000 10010000 cloneD 600 chr22 10011000 10015000 cloneE 300 chr22 10012000 10017000 cloneF 100 Click here to display this track in the Genome Browser. Step 6. (Optional) Share your annotation track with others |
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Sharing Your Annotation Track with Others |
To make your Genome Browser annotation track viewable by people on other machines or at other sites, follow the steps below. (Note that some of the URL examples in this section have been broken up into 2 lines for documentation display purposes). 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:
Combine the above pieces of information into a URL of the following format (the information specific to your annotation file is highlighted): Example 10: Step 3. Provide the URL to others. To upload a custom annotation track pointed to by a URL into the Genome Browser, paste the URL into the large text edit box on the Add Custom Tracks page, then click the Submit button. If you'd like to share your annotation track with a broader audience, send the URL for your track—along with a description of the format, methods, and data used—to the UCSC Genome mailing list genome@soe.ucsc.edu. |