Hi Dave, Perhaps the bedItemOverlapCount utility in our source tree can help you obtain the visualization you are looking for. A pre-compiled version can be found here: http://hgdownload.cse.ucsc.edu/admin/exe (note we only have versions complied for linux and MacOSX). One of the arguments for this program is the chromosome sizes, which are typically accessed from a mysql database. To bypass this have your database be "none" (you do need to give it something for this argument) and then specify the -chromSize= to be a file containing the chrom sizes, which can be found here for mm9: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ chromInfo.txt.gz.
This will output a bedGraph file. If your data is genome-wide, you should then convert it to a bigWig using the bedGraphToBigWig utility, also available in the same location mentioned above. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/24/10 7:23 AM, David A. wrote: > Dear list, > > I am trying to visualize alignment of my Illumina reads in the Genome > Browser. The result I am trying to get is a track where I can see the reads > piling up, as if they were peaks of alignment, as is shown in many articles > and presentations. To do so, as I want to load alignment against the whole > mouse genome, I transformed my Illumina _sorted.txt to BED format and this > BED format to BigBed format so that transfering data to the Genome Browser > was faster. But I am getting just plain rectangular boxes at the given > positions of alignment and not a nice shaped peak that would allow me to > rougly compare peak heights visually. > > Where am I going wrong? > > Thanks for your help > > Dave > > _________________________________________________________________ > Hotmail: Trusted email with powerful SPAM protection. > https://signup.live.com/signup.aspx?id=60969 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
