On Tue, Nov 4, 2008 at 12:13 PM, Simon Anders <[EMAIL PROTECTED]> wrote:
> Hi, > > Sean Davis wrote: > > MAQ, gmap, blat, and bowtie (and maybe SOAP--we do not use it) will > output > > multiple hits if you like. The manuals for these alignment algorithms > will > > give you details. > > A minor correction: As far as I understood from reading many posts about > the subject on the Maq-help mailing list, Maq cannot output multiple > hits. If it encounters a read that maps well to multiple locations it > will give one of the possible alignments, chosen at random. The > alignment quality is then set to a low value. Furthermore, one of the > output column counts how often the first 24 bp of the read could be > aligned to the reference. (That this information applies only to the > first 24bp and not to the whole read has technical reasons; Maq would be > way less efficient otherwise.) > That used to be true, but I think things have changed (correct me if I am wrong on this). http://sourceforge.net/project/shownotes.php?group_id=191815&release_id=595346 Sean > > +--- > | Dr. Simon Anders, Dipl. Phys. > | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK > | office phone +44-1223-494478, mobile phone +44-7505-841692 > | preferred (permanent) e-mail: [EMAIL PROTECTED] > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
