Dear Sirs I would like to get a copy of all the known genes for a particular chromosome, extract all the exons and then use this data for another application. I decided to use the UCSC genes as they are a nice conservative set of gene predictions for this project.
So using the Table browser, I selected genome: Mouse, assembly: July 2007, groups: Genes and Gene Prediction tracks, track: UCSC genes, table: known genes, which appeared to have all the information I was looking for. I then selected region, highlighted position and typed in chr19. I selected to save the output to a file and I used the ftp site to select the mouse chromosome sequences. The intention was to get a copy of all UCSC genes that are annotated as being on Mouse chromosome 19. When I examined the output from Table browser, I found a number of genes near the start of the chromosome, however when I looked at this data for the same build in the Genome Browser, no such genes were shown in the UCSC genes track. So for example, there are 267 rows of genes from the Table Browse that are not displayed in the Genome browser. Extracting a number of these from the corresponding chromosome files, I find the sequences are primarily Ns, so that does not seem correct. My questions are is this the best strategy to go about extracting this information? Why are there apparently genes located in the first 3 million bases of mouse chromosome 19 with Table Browser but not shown with Genome Browser? Am I misunderstanding something in setting up the query? Thanks kevin Kevin Clancy, PhD Senior Scientist, Informatic Sciences Invitrogen Corp Carlsbad, CA 92008 Phone: (768) 268 8356 Email: [email protected] _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
