creating URL for direct gene location

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David Hoover

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Jan 19, 2016, 3:52:34 PM1/19/16
to genome...@soe.ucsc.edu
When we construct a URL to link to the browser using a gene ID, the main Genome Browser site generates a single hit on the UCSC genes and RefSeq tracks, which leads directly to the browser image.

http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg19&position=NM_013319+RefSeq&hgt.positionInput=NM_013319+RefSeq&Submit=submit
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg19&position=UBIAD1+RefSeq

However, on our mirror, we get two hits for UCSC and two hits for RefSeq:

https://hpcwebapps.cit.nih.gov/eyebrowse/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg19&position=NM_013319+RefSeq&hgt.positionInput=NM_013319+RefSeq&Submit=submit
https://hpcwebapps.cit.nih.gov/eyebrowse/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg19&position=UBIAD1+RefSeq

Any ideas why there would repeats of the positional links?

Also, is there a better way of constructing a URL that, given a gene ID, can lead directly to a browser image page, rather than the multiple choice link page?

Thanks,
David Hoover
HPC @ NIH

Luvina Guruvadoo

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Jan 25, 2016, 3:05:12 PM1/25/16
to David Hoover, genome...@soe.ucsc.edu
Hello David,

Thanks for your question. The URL you have constructed is correct; if you have the unique gene ID and other parameters specified in your URL, only one result should open in the browser. Try this query on your mirror to see what might be happening:
mysql --user=genomep --password --host=genome-mysql.cse.ucsc.edu      -A -e 'select count(*) from trackDb;' hg38
Enter password: (enter your password)
Let us know if you are still experiencing difficulties.

If you have any further questions, please reply to genome...@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

--
Luvina Guruvadoo
UCSC Genome Browser

http://genome.ucsc.edu





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--
Luvina Guruvadoo
UCSC Genome Browser

http://genome.ucsc.edu


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