On Tue, Nov 4, 2008 at 12:13 PM, Simon Anders <anders@ebi.ac.uk> 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: sanders@fs.tum.de
>
>
>
>

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