Load custom track via URL with non-default position

[Thomas Sibley]

Hi,

I’m constructing URLs to load a custom track. The track contains a “browser position” line to set a default position. This works great!

However, any “position” parameter in the URL seems to be ignored, so I can’t construct a URL which loads the track to a non-default position. For example:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed

loads up at the default position defined by the bed file, and:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed&position=chrX

does the same, despite the position=chrX parameter. I’d expect it to display chrX, since an explicit position was given.

I’ve read the custom track documentation <http://genome.ucsc.edu/goldenPath/help/customTrack.html> which seems to suggest that providing a position should work.

Is the current behavior the desired one, or is it supposed to work as I expect?

Cheers,
Thomas

[Luvina Guruvadoo]

Hello Thomas,

Thank you for your question. You are correct; if the "position" parameter is defined in the URL, the browser will open to the specified location. However, if you take a look at the example custom track you provided in your email (http://genome.ucsc.edu/goldenPath/help/test.bed), the browser position has already been defined in the first line: browser position chr22:20100000-20140000. This overrides the URL parameter. If you upload the custom track without the browser position line and include the position parameter in your URL (such as chrX), the browser opens to the desired location. I hope this helps clarify things.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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