Hello Leo, Sorry to hear you're having trouble displaying your data. Unfortunately, it seems that you have been caught in an in-between state. The latest version of our big* tools from our source tree are not compatible with the display in the browser. Later today, we will be updating the software on the genome browser -- this should solve the problem. If not, please feel free to write back to this list.
Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu ----- Original Message ----- From: "Leo J. LEE" <[email protected]> To: [email protected] Sent: Monday, December 7, 2009 5:05:02 PM GMT -08:00 US/Canada Pacific Subject: [Genome] trouble creating BigWig from bedGraph files Hi, I have downloaded the latest version of bedGraphToBigWig (Linux 64-bit) but was not able to get it working properly (after spending quite some time). Here is a small example of what I did: First I created a small bedGraph file "cerebellum_coverage_small.wig" at <http://www.psi.toronto.edu/~ljlee/UCSC/> and it displayed properly in the genome browser. After removing the first line and rename it as "cerebellum_coverage_small.bedGraph", I ran "bedGraphToBigWig cerebellum_coverage_small.bedGraph hg19.chrom.sizes cerebellum_coverage_small.bw" and it completed successfully. However, when I try to add a custom track with the following track line: "track type=bigWig name="Cerebellum_cover" description="Read coverage in Cerebellum" color=255,0,0 bigDataUrl=http://www.psi.toronto.edu/~ljlee/UCSC/cerebellum_coverage_small.bw";, I got the following error message: "Error udc couldn't read 8 bytes from http://www.psi.toronto.edu/~ljlee/UCSC/cerebellum_coverage_small.bw, did read 0" It seems that the genome browser is having trouble reading the file but I can access it perfectly from the Internet (all files in this example are available at http://www.psi.toronto.edu/~ljlee/UCSC/). Could somebody help me to take a look please? BTW, I also tried running bedGraphToBigWig on the compressed version of the file but I got the following message: Success Can't lineFileSeek on a compressed file: cerebellum_coverage_small.bedGraph.gz and the resulting .bw file is essentially empty. Hopefully I didn't do anything too stupid... Thanks a lot for your help! -- Leo _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
