Hello, Thank you for letting know about the performance issue. Please use the http://genome-test.cse.ucsc.edu/ server for this type of comparison for now or limit comparisons per-chromosome on the main http://genome.ucsc.edu/ server. We have investigated and come up with a solution that will be on the main server as soon as possible.
Thank you again for providing such clear examples. Very helpful! Jennifer Jackson UCSC Genome Bioinformatics Group Khrebtukova, Irina wrote: > I'm trying to use Table browser to get BED tracks of Base-pair-wise > intersection of various tracks. For example, intersecting dbSNP and > knownGene exons to get a track of genome bases in dbSNP covered by any > known genes exon. This used to work for any track but now it works for > small tracks only. Even intersecting known gene track to itself to get > bed track of genome bases covered by known genes exons does not work any > more - the file is truncated: > > > > $ tail knownGenes_bitwiseIntersect > > chr11 95160435 95160490 chr11.9285 > > chr11 95161310 95161375 chr11.9286 > > chr11 95162203 95162602 chr11.9287 > > chr11 95163289 95163555 chr11.9288 > > chr11 95172043 95172200 chr11.9289 > > chr11 95185715 95185923 chr11.9290 > > chr11 95186279 95186401 chr11.9291 > > ------------------------------------------------------------------------ > --- > > Allocated too much memory - more than 6,442,450,941 bytes > (6,442,483,623) > > ------------------------------------------------------------------------ > --- > > > > Is it possible for me to do such intersection locally? I mean without > setting up whole local browser. Or may be you can suggest some other way > around. > > > > Thanks! > > > > Irina Khrebtukova, PhD > > Sr. Staff Bioinformatics Scientist > > Gene Expression Applications R&D > > > > Illumina Inc. > > 25861 Industrial Blvd., > > Hayward, CA 94545 > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
