Hello Pei-Yi, The Genome Browser (at UCSC web server site) cannot actually see your "C" drive. When you select a file to upload as a custom track, your web browser reads the file and then transmits its contents via http to our server. There is no information sent about where that file is located on your system, or how the rest of the world can access your system. (This is a good thing!)
While we have the Custom Track function to support users to upload modest size data for visualization using UCSC Genome Browser, we are aware of the growing demand of groups around the world that want to use our Browser with a large amount of local data without requiring significant bioinformatics support. Our engineers are exploring various ways to eventually enable that. So stay tuned. -- Brooke Rhead UCSC Genome Bioinformatics Group Pei-Yi Tan wrote on 12/13/08 8:16 AM: > Brooke, > > Since UCSC Genome Browser can allow users to upload and submit a local custom > annotation text file through "Add Custom Track" that indicates the browser > has the ability to locate and read users' local (C: drive for example) > annotation file then populate the information into the Genome Browser. > > I would like to request the same feature implemented for constructing a URL > that will link this annotation file to the Genome Browser; allowing > hgt.customText=C:\xxx.txt specified. > > http://genome.ucsc.edu/cgi-bin/hgTracks?org=organism_name&; > position=chr_position&hgt.customText=URL. > > Thank you, > Pei-Yi > ________________________________________ > From: Brooke Rhead [[email protected]] > Sent: Friday, December 12, 2008 5:40 PM > To: Pei-Yi Tan > Cc: rhea >> Brooke Rhead > Subject: Re: [Genome] Unable to display custom tracks via URL > > Hi Pei-Yi, > > No, UCSC does not provide a place to host data for users that is > accessible from a URL. However, if you upload your data as a custom > track and then save it in a session: > > http://genome.ucsc.edu/cgi-bin/hgSession > > The custom track will persist for a much longer period of time than a > regular custom track. The session can also be shared. > > You might also try something like Google sites (sites.google.com) for > hosting your data. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 12/12/08 11:58, Pei-Yi Tan wrote: > >> Thank you very much for your prompt reply. >> I see my problem is my formatted annotation file is not loaded on a >> > web site. > >> Does ucsc genome browser site has a location which allows users to >> > upload the custom annotation file to. > >> Thanks, >> Pei-Yi >> >> -----Original Message----- >> From: Brooke Rhead [mailto:[email protected]] >> Sent: Friday, December 12, 2008 1:56 PM >> To: Pei-Yi Tan >> Cc: [email protected] >> Subject: Re: [Genome] Unable to display custom tracks via URL >> >> Hello Pei-Yi, >> >> The error message you are seeing is not the correct error message. We >> discovered a bug recently that causes any type of custom track error to >> give the message "Unknown encodePeak type". We have fixed the bug on >> our test site, here: >> >> http://genome-test.cse.ucsc.edu >> >> Note that the test site has a lot of untested and experimental data, so >> use caution if you are retrieving data from it. The fix will be on our >> public site (genome.ucsc.edu) in about a week. >> >> In the meantime, you can use the test site to get a more informative >> error message. >> >> I tried your example url with the test site in place of the regular site: >> http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr14&hgt.customText=c:\customtrack.txt >> and this error message was generated: >> >> Unrecognized format line 1 of custom track: c:\customtrack.txt (note: >> chrom names are case sensitive) >> >> Here are a couple of resources that might help you fix the problem you >> are seeing: >> >> http://genome.ucsc.edu/goldenPath/help/customTrack.html#SHARE >> http://www.soe.ucsc.edu/pipermail/genome/2004-July/005017.html >> >> I hope this is helpful, and I apologize for the inconvenience caused by >> the misleading error message. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 12/12/08 09:43, Pei-Yi Tan wrote: >> >>> Genome location: chr14:19336854-106356482 >>> >>> >>> I am able to manually upload and successfully submit the attached >>> file >>> >> from "Add custom track", but am getting "Unknown encodePeak type" error >> message when launching custom tracks via below URL: >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr14&hgt.customText=c:\customtrack.txt >> >> >>> Pei-Yi Tan >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome >>> _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
