Hello Chris, Apologies for the delay in replying. Could you please send me the name(s) of the tables you were extracting BED output from as well as a sample of the output so that I can try to reproduce the issue. Please send this to me and not to the list.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 01/27/11 22:37, Chris Dias wrote: > Hello, > I used the UCSC table browser to extract a BED file with exon coordinates > for a list of genes. > When I tried working with the file, I realized that there was an error in > the coordinates. > Lines x to y refer to gene NM_001848 (COL6A2). > While the RefSeq gene name is correct in the file (NM_001848_exon_#), the > coordinates that are associated with that gene map to NM_206962.1, an > adjacent gene (PRMT2) on chromosome 21. > I further went on to notice that the file contained aditional COL6A2 > transcripts which coordinates mapped outside chromosome 21, therefore I was > constantly getting an error message when trying to use this file. > When I made a query for the COL6A2 coordinates with the one isolated gene > identifier, the BED file output was correct. I.e., I do not understand why > the original output did not work correctly. > Thank-you, > Chris Dias > UBC > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
