displaying of wrong genomic location
Lisette Stolk
Dear Sir/Madam,
This afternoon I encountered some problems when displaying the genomic location of a sequence I searched in BLAT.
When searching the sequence (approximately 40bp long) I got the correct position on chr 15.
When zooming out to search for the nearest exon, I was redirected to a gene on chromosome 8. And when zooming out a 2nd time, I was redirected to yet another gene and now on chr 13.
This is something I have experienced before, at that time I got back the search results for one of my colleagues who was using the Genome browser at the same time (and who was in the same room in the office as I am).
So today I also asked my colleagues if someone was searching for these 2 genes and there was 1, in a different building this time.
Do you have any clue how this is possible?
I tried to search your website, your archives and the wiki, but I did not know how to exactly phrase this problem, so I could not find any information.
Best regards,
Lisette Stolk
Christopher Lee
Thank you for your question about zooming and location errors. Is it
possible that you and your colleagues were sharing links with each
other, and that the links had an hgsid= parameter in the URL? So maybe
you shared a link to blat results like:
"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr7%3A128251991%2D128252162&
hgsid=585119239_xha1IwBQpVcVGVnTSb1QEd1GSfvl"
The hgsid parameter is specific to your particular browsing session on
the Genome Browser, and so if a link with an hgsid parameter is shared
with a colleague and they click the link and start making changes to
the view, then when you make changes to your view, the Genome Browser
makes the changes instead to the most recent state of the hgsid and
returns the associated view. For example, perhaps you send a link of
BLAT results to your colleague, then on their computer they click the
link but then go to a different gene, and then from your computer you
zoom out from the original BLAT result. Because our server considers
the different gene your colleague was looking at as the most recent
state of the hgsid, the Genome Browser will zoom out from that
location, and then return the view to you.
Because of this behavior we recommend that people not share links
(especially not with the hgsid parameter included), and instead use
what we call a session to share views with one another. For more
information on creating and using sessions, please read the Sessions
User Guide:
http://genome-euro.ucsc.edu/goldenPath/help/hgSessionHelp.html
Additionally, since you and your colleagues are all likely using the
same hgsid at this point, could you please click the Home icon from
the top blue bar to navigate back to the Genome Browser home page and
then go back to the track view? This way each of you will have
different hgsid's and can make changes and navigate around without
interfering with each others sessions.
I hope this helps, and please let us know if you have any further questions!
Thank you again for your inquiry and using the UCSC Genome Browser. 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.
Christopher Lee
UCSC Genomics Institute
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Christopher Lee
"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr7%3A128251991%2D128252162& hgsid=585119239_xha1IwBQpVcVGVnTSb1QEd1GSfvl"