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.
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. If not, I suggest you try to troubleshoot your BOWTIE pipeline. I hope this helps. Please contact us via the mailing list if you have further questions. Luvina Guruvadoo UCSC Genome Bioinformatics Group Duke wrote: > On 1/19/11 4:19 PM, Luvina Guruvadoo wrote: >> Hello D., >> >> Thanks for your inquiry. The letters (A, C, T, G) refer to bases that >> do not match the reference assembly. "N" means "nucleotide" >> (unknown), so it is always a mismatch. By default, mismatching bases >> are highlighted red in the display. > > Hi Luvina, > > Thanks for your response. I am still confused. If A, C, T, G are bases > that do not match the reference, then are they mismatches? If they are > mismatches, then why they are in white (please see > http://img4.imageshack.us/img4/4976/screenshot20110119at301.png) > instead of red? Also, if all those letters (A, C, T, G, N) are > mismatches, it even confuses me more since the track shown in the > screenshot was aligned with Bowtie and two mismatches max per read > (where as there are some reads with 5 mismatches). > > Please advise, > > Thanks, > > D. > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
