Hello Elizabeth, The solution is to give a unique "name" identifier to each element in the BED file, rather than giving each the same "name" identifier, for your case, a "3".
When I loaded chr22 sample data in the original format with name = "3", I experienced the same browser behavior as you did. When I named the elements on chrom 22 with identifiers 1-9, the issue was resolved. I will pass this one to the development team for review since this might not be an intentional constraint. Many native browser tracks have duplicated names, although they are not in BED format. As a side issue, you do have coordinates that extend outside of the chromosomes actual known sequence, but this does not seem to be an issue. Just something to be aware of. Please try the unique names and see if the problem is eliminated for you as well. Hopefully this helps! Thank you for sending your question along with such a clear explanation and with sample data. This was very useful. Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/17/10 7:24 AM, Wohler, Elizabeth wrote: > Hello, > > I am experiencing a problem with one of our custom bed file tracks that we > have developed. When the track is displayed in the Genome Browser (March 2006 > build/NCBI36), each bar appears to display correctly. However, when I click > on some of the bars, the base pair position that is listed is incorrect for > some of the bars. I have attached the custom .bed file for you to look at to > see the same problem. For example, on chromosome 22 there are nine bars > present on the chromosome. The base pair locations for bars #4 and 8 are > incorrect, even though they are listed correctly in the .bed file and are > displaying correctly in the Genome Browser. The problem seems to be resolved > when I take away the thickStart and thickEND and just use a simplified .bed > file, however I would like to continue to use the colored bars and cannot do > so when it is in a simplified form. I have a few other custom files that also > are showing this same effect, but I have attached this one as an example. > > Thank you very much for your assistance, > Elizabeth Wohler > > Kennedy Krieger Institute > 707 N Broadway > Baltimore, MD 21205 > (443) 923-2785 > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health > Information. Please note that e-mail is not necessarily confidential or > secure. Your use of e-mail constitutes your acknowledgment of these > confidentiality and security limitations. If you are not the intended > recipient, be advised that any unauthorized use, disclosure, copying, > distribution, or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this e-mail in > error, please immediately notify the sender via telephone or return e-mail. > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
