Hello, All data tracks are mapped to genomic. One method would be to export the coordinates of mapped genes and compare to the coordinates for your features with your own tools. Use the Table browser or ftp from the Downloads server.
For example, if using the Table browser and the UCSC Genes track, set output as "selected fields from primary and related tables", name, and download. The primary table, knownGene, should be joined with the table kgProtAlias to obtain the gene name as displayed in the Browser. Data columns of interest for you would include: knownGene.strand, knownGene.txStart, knownGene.txEnd and kgProtAlias.displayID. Some coordinate help: Instead of downloading, another option to try is to send the same data to Galaxy. Also send your custom track data. Then use the function: Operate on Genomic Intervals -> fetch closest feature. It may provide the results you want. Click on the Help link (top black bar) for questions/tutorials. Jennifer Jackson UCSC Genome Bioinformatics Group Ingrid Lindquist wrote: > Hello, > I am visualizing copy number variation in a set of data on genome browser. > Some of these are intergenic and I would like to calculate the distance > between the ends of the CNVs and the closest genes. This would mean for the > 3' end of the CNV, i would know how many bp there are between the 3' end of > the cnv and the 5' of the closest upstream gene. Likewise for the 5' end > of the CNV and the 3' of the next gene. How can I export this data from the > UCSC genomebrowser site? I would want to collet the gene name as well. > > Let me know, I can't seem to find it on the FAQ page, even though someone > probably has asked it before. > > Thanks > > Ingrid > > > Ingrid Lindquist > Class of 2010 > [email protected] > 505.310.8932 > ----------------- > Bucan Laboratory > University of Pennsylvania > Department of Genetics > Philadelphia, PA > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
