Adding Custom Tracks

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nkokan
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Joined: Fri Jun 06, 2008 5:24 pm
Location: Cardinal Stritch University

Adding Custom Tracks

Post by nkokan » Wed Apr 06, 2011 2:13 am

How can I add custom tracks in the Genome Browser for annotations? I see the custom tracks of the gene from the Gene Model Checker but not in the mirror browser site. I do not understand the file formats for the upload. Are there instructions for this somewhere?
nkokan
Nighat P Kokan, PhD
Associate Professor
Department of Natural Sciences
Cardinal Stritch University
Milwaukee, WI 53217
414.410.4138

cshaffer
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Location: Washington University in St Louis
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Re: Adding Custom Tracks

Post by cshaffer » Wed Apr 06, 2011 5:49 pm

There is indeed a way to add custom tracks. To start the process you want to use the "add custom tracks" button on the genome gateway page to get to the upload page. Click the "genome browser" link on the front page to get to the genome gateway page.

When you get to the upload custom tracks page you will either need to paste in the data, or select a file to upload. The whole process is pretty picky about everything being in exactly the correct format. The supported formats are discussed here http://gander.wustl.edu/goldenPath/help ... Track.html. Not all the links on that page work, you will need to go to the help page at santa cruz (http://genome.ucsc.edu/goldenPath/help/customTrack.html) if you want to see working examples.

Some programs will create a compatible file that you can upload directly, many do not (BLAST at NCBI, for example).

If you are trying to do something by hand you will probably want to use the BED format, it only requires the header, and then 3 entries per line. You can have more information on each line but they are all optional and the track will work just fine with just the 3 entries.

If you have a specific task you are thinking about feel free to post follow-up questions with more specific answers.

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