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Old 09-14-2011, 12:33 PM   #1
zhenhua
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Location: Boston

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

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'?
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Old 09-14-2011, 12:38 PM   #2
westerman
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Location: Purdue University, Indiana, USA

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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

Last edited by westerman; 09-14-2011 at 12:43 PM. Reason: Added in 'not extensively' to clarify my Tophat usage.
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