Hi Duke, This error that you are seeing is possibly from the fact that display code wasn't able to handle the lack of query sequence. That has been fixed in the latest code and will go out in the next tri-weekly release which which is announced on our genome-mirror mailing list (https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror) if you would like to be notified. Along with release announcements, there is some traffic on this mailing list that is very specific to administering a local installation.
Also, for large data sets we highly recommend using the bigBed format: http://genome.ucsc.edu/goldenPath/help/bigBed.html Sorry for the inconvenience. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Duke <[email protected]> Date: Thu, Aug 4, 2011 at 10:28 AM Subject: [Genome] BAM not support zero size block? To: "[email protected]" <[email protected]> Hi, Please correct me if I am wrong. I have some insertion/deletion bed output from TopHat, and uploading these files to UCSC Genome Browser was fine. Then I tried to convert to BAM format (using bedToBam in BEDTools package) and put the link on the browser. I got error: baseColorDrawSetup: -: mRNA size (0) != psl qSize (2) Does that mean BAM does not support 0-size blocks? If not, then please explain to me why I had the above error. Thanks D. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
