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

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