Hi Niki, It's possible that your BED file may be too large. We have seen problems similar to what you're describing when users attempt to upload extremely large files. You may want to consider using bigBed format instead. The following page provides more details on this format: http://genome.ucsc.edu/goldenPath/help/bigBed.html
Please contact us again at [email protected] if you are still experiencing difficulties. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 4/5/2012 10:26 AM, Rodoniki Athanasiadou wrote: > Hi > I am trying to upload my high-throughput sequencing data to the UCSC genome > browser as a custom track. > > I upload a BED file containing alignment coordinates for 4 samples (track > name defined at the begining of each data set). The coordinates are sorted in > ascending order. > > After running for a little while with apparent high " Data sent" activity > (Activity Monitor Mac OS X) I get this error page: > *Can't start querry:select genome from dbDb where name=sacCer3 > *mySQL error 2013: Lost Connection to MySQL server during query > > my browser and track lines look like this: > browser position chrXI:510000-520000 > browser hide all > track name="somename" description="somedescription" visibility=2 > colorByStrand="255,0,0 0,0,255" > > I would appreciate any help with this > > Thank you > Niki Athanasiadou, PhD > > Gresham Lab > NYU > Center for Genomics and Systems Biology > 12 Waverly Place > NY10003 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
