What you have are the mapping coordinates of your reads, I am assuming. But it sounds like you are trying to generate a coverage plot, so for this what you want is a bedgraph or wig track, which basically has a position and a value corresponding to the number of reads covering that position, as opposed to the reads themselves. This will basically plot as a continuous function.
You can then adjust the smoothness and range etc to your fancy (see the track data types under the faqs for more information). If your reads are already in bed format, the link below will be helpful in creating the bedgraph or wig track: http://code.google.com/p/bedtools/ good luck. On Thu, Jun 24, 2010 at 7:23 AM, David A. <[email protected]> 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
