Bowtie -n vs. -v, which one should we use?

[zhenhua]

I noticed that in Bowtie, the default is using -n, where it considering quality score. -v option does not consider quality score.

However, in Tophat, which calls Bowtie for mapping, the default is using '-v' when it calls Bowtie. I am just wondering why Tophat uses '-v' option when calling Bowtie, not '-n'?

[westerman]

I do not use TopHat (at least not extensively) so can not say for sure but I suspect that it is because -n vs. -v is more than just 'use quality' vs. 'do not use quality'. Tophat probably wants the more simple and less filtered results from '-v'. See: http://bowtie-bio.sourceforge.net/ma...alignment-mode