Hello Pat, We have read through all of your emails and understand that your team is frustrated. In particular, you mention that the problem was present in a Session, but was not present outside of a Session for you. Also that another user had the problem persistently.
Some options: 1) Re-create a new Session 2) Try a "cart reset" when working outside of a Session. There is a link in the top paragraph of the gateway page to do this, or simply use this url: http://genome.ucsc.edu/cgi-bin/cartReset (note that all saved data/settings will be removed). Sometimes old saved variables can cause strange browser behavior. These are rare, and we hunt them down whenever possible, but this is good advice to follow whenever the view or data is unexpected. 3) Or, best, reset your cart, then create a new Session and see what happens. We have high confidence that the sequence data for Human May 2004 (hg17) assembly has not changed on the main genome site. By checking the time stamps on the files in Downloads and for Tracks/tables in the browser, the data has been updated only as recored in the Release Log. For the key files pertaining to chromosome length (chromosome files in Downloads, Assembly and Chromosome Band tracks in the Genome Browser) the dates are from 2004. Please try a test with a cart-reset and a new Session and please let us know if you continue to experience problems, Jennifer Jackson UCSC Genome Bioinformatics Group Gonzales, Patrick R. wrote: > Xq28 [hg17] annotation has definitely changed on your end. Up until > recently, Xq/Yq PAR2 was located at chrX:154494747-154824267. Now, in > UCSC hg17, the last nucleotide on Xq28 is 154824264. This is likely the > source of errors we are seeing. ??? > > > Pat > > Patrick R. Gonzales, MS, CLSp(CG) > Development Technologist I > Array CGH-Cytogenetics Laboratory > Phone: (507)284-8338 > >> Fax: (507)284-0043 >> > E-mail: [email protected] > ________________________________ > Mayo Clinic > 200 First Street SW > Rochester, MN 55905 > www.mayoclinic.org > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Tuesday, May 26, 2009 5:23 PM > To: Gonzales, Patrick R. > Cc: [email protected]; Seger, Pamela R. > Subject: Re: [Genome] Problems with Xq28 in hg17/May 2004 > > Hello, > We are unable to duplicate. Would you be able to provide a few more > details? > > 1) are you using the UCSC Browser at http://genome.ucsc.edu ? or a > different location/local mirror? > 2) are you just entering "Xq28" into the position/search box? Or actual > coordinates? If coordinates, double check that the assembly is set > correctly. The new human assembly hg19 (Feb. 2009) was recently added to > > the gateway page and may cause some confusion. > > Thank you, > Jennifer Jackson > > Gonzales, Patrick R. wrote: > >> Hello: >> >> When we try to view human Xq28 in UCSC hg17/May 2004, we get this >> > error > >> message below the ChrX idiogram display... >> >> nib read past end of file (154824267 154824264) in file: >> /gbdb/hg17/nib/chrX.nib >> >> Can you help with this? Thanks. >> >> Pat >> >> Patrick R. Gonzales, MS, CLSp(CG) >> Development Technologist I >> Array CGH-Cytogenetics Laboratory >> Phone: (507)284-8338 >> >> >>> Fax: (507)284-0043 >>> >>> >> E-mail: [email protected] >> ________________________________ >> Mayo Clinic >> 200 First Street SW >> Rochester, MN 55905 >> www.mayoclinic.org >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
