Hi, On Thu, Feb 10, 2011 at 8:48 PM, Paul Leo <[email protected]> wrote: > > Also if your alignments are in BAM format , so can use Rsamtools to > extract that region. Inspection of the cigar will tell you which reads > aligned perfectly. That would be an extremely fast calculation.
Actually, I'm not sure that that's true, is it? Don't cigar strings only really tell you about indels? Say you have two reads, both 38bp long. If one aligns perfectly, its cigar is 38M If the other aligns with 1 mismatch, its still 38M. You can use the NM tag if you're after 'perfect matches', though ... -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
