Hey Jessica, Thanks for sending me your whole data file offline. It looks like there's a difference between what you excerpted in your mail below and what's in your original data file. The difference is in the 11th field of your bed file where the blockSizes go. In your excerpted sample you have 1,7000 but in your original file you have 17, 000 which is resulting in the zero length blocks you're seeing in your bigBed display.
I hope this resolves your problem. Thanks for your efforts in reporting this, we're actively looking for bigBed problems as part of our roll out. brian On Tue, Aug 18, 2009 at 8:13 AM, Jessica Wasserscheid < [email protected]> wrote: > > Hi, > > I am currently trying to convert my custom tracks into bigBed, to make > it faster. > But I came across a bug. I made a screenshot of my browser view below, > it contains the bigBed version of tracks (called "2Q1M") and I also > added a few line of the original BED custom tracks manually (User > Supplied Track), so that you can see how it's supposed to look. > The thick end on the 3' side for all my minus strand tracks disappears > in the bigBed format. > > > > When clicking on one of these (CH252-438C22-T7 here), the coordinates > are right, only the thicker black square doesn't appear : > > > > > Here are the BED lines : > chr3 46428184 46538284 CH252-286E21-Sp6 1000 - > 46428184 46538284 0 2 1,7000 0,103100 > chr3 46445463 46555563 CH252-322D14-T7 1000 - > 46445463 46555563 0 2 1,7000 0,103100 > chr3 46458565 46568665 CH252-130I24-Sp6 1000 - > 46458565 46568665 0 2 1,7000 0,103100 > chr3 46458567 46568667 CH252-356E7-T7 1000 - > 46458567 46568667 0 2 1,7000 0,103100 > chr3 46494117 46604217 CH252-410B16-T7 1000 - > 46494117 46604217 0 2 1,7000 0,103100 > chr3 46497854 46607954 CH252-526M24-T7 1000 - > 46497854 46607954 0 2 1,7000 0,103100 > chr3 46510064 46620164 CH252-254O3-Sp6 1000 - > 46510064 46620164 0 2 1,7000 0,103100 > chr3 46513224 46623324 CH252-457N6-Sp6 1000 - > 46513224 46623324 0 2 1,7000 0,103100 > chr3 46537860 46647960 CH252-438C22-T7 1000 - > 46537860 46647960 0 2 1,7000 0,103100 > > It's also considerably slow, but maybe the server is just having a hard > time today. > > Thanks for your help, > > Jessica > > -- > Jessica Wasserscheid > Bioinformatician, Vervet Monkey Genomics Project > http://www.genomequebec.mcgill.ca/compgen/submit_db/vervet_project > McGill University & Genome Quebec Innovation Center > 740 Dr. Penfield Avenue Room 7211 > Montreal, Quebec Canada, H3A 1A4 > > Email : [email protected] > Phone : (001) 514-398-3311 #00476 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
