[Bioc-sig-seq] processing alignments

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Feb 11 02:58:51 CET 2011


On Thu, Feb 10, 2011 at 8:48 PM, Paul Leo <p.leo at uq.edu.au> 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

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