Hi Luvina, On 1/20/11 7:24 PM, Luvina Guruvadoo wrote: > Hello Duke, > > My apologies for not clarifying in my previous email. When zoomed in > to base level, the mismatching bases appear white. When zoomed out, > the positions of the mismatching bases are represented by a thin red > line. >
Thanks. I also recognized this point. > As for the screenshot you provided, is it possible that the alignment > was made to a different assembly (not hg19)? If so, this may be why > you are seeing more than two mismatches per read. I dont really understand this point. The data I work with is mouse (mm9), and it was aligned with bowtie with reference mm9. Did you mean if a data aligned to one species will be shown like that if uploaded to different species? > If not, I suggest you try to troubleshoot your BOWTIE pipeline. Anyway, I think there might be something with our bowtie pipeline. We will have to carefully check it. Thanks, D. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
