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                | Frequently Asked Questions: Custom Annotation Tracks |  
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		    | Displaying personal annotation data in the Genome Browser |   |  |  
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			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. 
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		    | Adding a personal annotation track to the Genome Browser website |   |  |  
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			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.
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		    | Defining filter parameters for custom tracks |   |  |  
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			Question: "Is it possible to define a filter parameter for a custom track to 
			highlight certain features?"
 
			Response:This feature is not currently implemented.
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		    | Coloring a custom track using the useScore parameter |   |  |  
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			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.
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		    | Constructing a Genome Browser URL |   |  |  
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			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.
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		    | Using the hgsid parameter in a URL |   |  |  
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			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.
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		    | Creating a details page for a custom annotation track |   |  |  
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			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."
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		    | Custom annotation track troubleshooting |   |  |  
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			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.
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