Hi Gabriel, Thank you for bringing this our attention. We are currently working on a solution. The fix should be in place by the end of tomorrow. If you have any other problems, please feel free to contact the mail list again.
Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/24/10 7:53 AM, Gabriel Renaud wrote: > Hi, > I was looking at a few genes on the chimp genome. For example: > > refGene.txt:115 NM_001037299 chr1 + 44440530 44635826 > 44440530 44635826 10 > 44440530,44499084,44520194,44545087,44603658,44604593,44604966,44626277,44626655,44635737, > 44440648,44499132,44520237,44545182,44603724,44604689,44605153,44626424,44626802,44635826, > 0 ST3GAL3 cmpl incmpl 0,1,1,2,2,2,2,0,0,0, > refSeqAli.txt:115 1036 0 0 0 1 91 9 194260 > + NM_001037299 112801127 chr1 229974691 44440530 > 44635826 10 118,48,43,95,66,96,187,147,147,89, > 0,118,166,209,395,461,557,744,891,1038, > 44440530,44499084,44520194,44545087,44603658,44604593,44604966,44626277,44626655,44635737, > > The coordinates 44440530 44635826 are the same in both files. But > with very few genes we have the following discrepancy : > > refGene.txt:1002 NM_001079831 chr19 - 54736378 > 54737410 54736378 54737410 354736378,54736785,54737352, > 54736550,54736953,54737410, 0 CGB1 incmpl cmpl 1,1,0, > /storage/grenaud/.snpAnnon/panTro2/database/refSeqAli.txt:1002 398 > 1 0 0 0 0 2 634 - NM_001079831 399 0399 > chr19 64473437 54736377 54737410 3 173,168,58, > 0,173,341, 54736377,54736785,54737352, > > The start coordinate in refGene is 54736378 but it is 54736377 in > refSeqAli. Is there any reason for this or is this a bug ? > > Thank you, > > Gabriel > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
