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 | office phone +44-1223-494478, mobile phone +44-7505-841692 | preferred (permanent) e-mail: [EMAIL PROTECTED] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
