Hello David, Using the refFlat table with the complete gene structure will filter by exon. This seems to be what you want? If a probe does not map, then it is not in an existing exon.
If you want to get the coordinates of all probes, regardless of inclusion in a RefSeq exon, these are in the GNF Gene Altas 2 track tables. Other options: a) use the UCSC Genes track instead of RefSeq. UCSC Genes contains RefSeq plus more, see the track description for the content details. b) if you want to identify all problem that have any overlap with a RefSeq or UCSC Genes track (exon or intron), then strip the primary table (refGene/refFlat or knownGene) down to a BED6 file, which would remove the exon/intron structure leaving only the transcript's genome alignment footprint. To do this, save the table as a BED custom track in the Table browser, then save that BED custom track using "selected fields from primary and related tables" and only check the first six columns (ignoring the initial bin column if necessary). I am not sure if you are using the "Intersection" function or not, but this would be good to try, there are many options to specify the type of overlap that you want. Should you want output that has both the query (the probe) and the target (gene track) in each output line, then send both datasets over to Galaxy (check box at output stage), change file format to be "interval" using "edit" (click on the little pencil icon), and join the files based on overlap using the tool: "Operate on Genomic Intervals -> Join " or select the tool from this set that best meets your needs. Good luck and please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 8/31/10 10:33 AM, David Managadze wrote: > Hi, > I am working on human and mouse gene expression data, GNF Gene Atlas 2. > I need to get the multiple alignments of ONLY EXONS of my probesets. > In UCSC Table Browser, what I am trying to do is to somehow get the > coordinates of every exon of the human (and mouse) genome. > I used "RefSeq Genes -> refFlat" to get the RefSeq genes' exon coordinates > but the problem is that many of the probesets don't map to RefSeq genes that > makes such probesets useless. > > So, my question: how to map ALL my probesets to the human (and mouse) genome > and get the coordinates of ALL possible exons (that could possibly be found > for the genome)? > > Thanks for your help > > David > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
