[Bioc-sig-seq] ChIPseq, repeated regions and multiple matched tags

[Simon Anders]

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.)

  Simon


+---
| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
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