Hi Lucia, Unfortunately, the Table Browser intersects only the exons (or alignment blocks, etc) and not the entire span of genes. One of our engineers has this to say: A way around this would be to save a BED custom track file for the genes, and remove all columns after the first 4 or 6 columns, depending on whether a strand is needed downstream. Then upload the BED4 or BED6 version as a custom track, and intersect.
More information about Custom Tracks and BED format can be found on our help pages: http://genome.ucsc.edu/goldenPath/help/customTrack.html http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED I hope this helps answer your question. Please contact us again at [email protected] if you have additional questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 10/5/2011 7:04 AM, Lucia Franchini wrote: > Hi, > > I am trying to intersec two things in the Table Browser and I notice > the output I get is incorrect. I have tried to intersec Ref Seq genes > and Exapted Repeats (any overlap) and I am getting only 9 genes as a > result...and I know it can not be rigth! > I have using the human genome 2006 version. > > I hope you can help me, > > My best, > Lucía _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
