Hi Duke, > Did you mean > if a data aligned to one species will be shown like that if uploaded to > different species?
Yes, my colleague was trying to identify a possible reason why you might be seeing more than two mismatches per read. From the information you provided, however, this is not the issue with your data. It does seem that it is most likely an issue with your Bowtie pipeline. Best of luck! Katrina Learned UCSC Genome Bioinformatics Group Duke wrote, On 01/21/11 08:04: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
