Hi Kelly, The regions represented in pink on the Genome Graphs chromosome ideograms represent large gaps in the assembly. If you click on the pink region of one of the ideograms, you will be redirected to that region in the browser. If you turn on the "Gap" track (in the "Mapping and Sequencing Tracks" group), you'll see the large gaps spanning these regions. To see more information about a gap, click on the item. Most of these have a gap type of "short_arm," which are (from the Gap track description page): non-bridged long gaps on the short arm of the chromosome. Because there isn't sequence data for these regions of the assembly, data cannot be aligned to these regions.
Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Kelly Marie Bakulski wrote, On 04/08/11 08:25: > > Greetings, > > I have been uploading tracks to the UCSC Genome Browser Genome Graphs tool. > > > It does a great job of visualizing my data points throughout the genome. > However, certain regions show up as pink on the ideogram and when I upload > my data tracks all of my points that should map to that region are omitted. > > For example, the p arms of chromosomes 19, 20, and 21 are showing up as > pink instead of white. Also my data points that should be there are never > plotted, even though the rest of the genome looks fine. > > What's going on at these regions? Thanks for your help! > > Kelly Bakulski > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
