[Bioc-sig-seq] question about bowtie

[Joern Toedling]

Hello,

I think you should better ask questions of this kind to the developers of
Bowtie rather than on this mailing list. However, I believe all of your
questions are answered in the manual of bowtie. Basically you can customize
the report output by supplying additional arguments to the bowtie call. "-k"
specifies the maximum number of valid match postions for each read in the
output. If you set "-k 1" (the default) I think a random position is returned.
To my mind, the score is not directly given but the output column gives you
details which bases do not match and since you also have the quality
information of each base you can easily calculate the sum of mismatching base
qualities.
The tab-delimited output format (non-binary) can be read in by function 
readAligned(..., type="bowtie")
and the resulting object of class AlignedRead also stores the mismatch
information (at least in the current development version of package ShortRead).

Best regards,
Joern

On Mon, 6 Jul 2009 14:17:34 -0700, Bogdan Tanasa wrote
> Hi everyone.
> 
> I would appreciate to have your comments on the following : when aligning
> the solexa reads with bowtie,
> if a read aligns to multiple genomic regions, is the highest-scored location
> picked up in the final report
> 
> (i.e. when using --best option) ? And if a read aligns with the same 
> score to multiple regions, would it be possible to see the score of 
> the alignment and the differences in the score among multiple 
> regions ? In this last scenario, a randomly picked location among 
> the equally scored genomic locations is reported ?
> 
> thanks very much,
> 
> bogdan 

---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246926