Hello Vamsi, Unfortunately, the coordinates for transcript mappings cannot be created to mirror those at NCBI. The alignments in the UCSC Genome browser are independently generated when the track is created (see the track description for the full methods).
One option for you is to download the NCBI coordinates yourself and create a custom track. This could be loaded back into the UCSC Browser and viewed along with the rest of our annotation. Custom track help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Our apologies for the inconvenience. But, we hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 6/11/10 3:45 AM, Vamsi Veeramachaneni wrote: > Hi, > > I downloaded the hg19 refFlat.txt.gz file from UCSC > (ftp://genome-ftp.cse.ucsc.edu/goldenPath/hg18/database/refFlat.txt.gz). It > has multiple lines for a single gene. For instance, the command: > > % grep -e DEFB106A -e DEFB106B refFlat.txt > > generates the four lines: > > DEFB106A NM_152251 chr8 - 7340025 7343909 7340125 > 7343904 2 7340025,7343855, 7340274,7343909, > DEFB106A NM_152251 chr8 + 7682693 7686575 7682698 > 7686475 2 7682693,7686326, 7682747,7686575, > DEFB106B NM_001040704 chr8 - 7340025 7343909 7340125 > 7343904 2 7340025,7343855, 7340274,7343909, > DEFB106B NM_001040704 chr8 + 7682693 7686575 7682698 > 7686475 2 7682693,7686326, 7682747,7686575, > > In other words, DEFB106A and DEFB106B have exactly the same annotation. I > realize this is because of duplicate regions, but the co-ordinates at NCBI > are: > * DEFB106A as Chromosome 8 (7682694..7686575) > * DEFB106B as Chromosome 8 (7340026..7343909, complement) > > Is there any way of getting the refFlat file with only the NCBI version of > the gene co-ordinates (or as close to those coordinates as possible) ? > > Thanks, > Vamsi > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
