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09-14-2011, 12:33 PM
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#1 |
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Junior Member
Location: Boston Join Date: Jul 2011
Posts: 1
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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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09-14-2011, 12:38 PM
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#2 |
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Rick Westerman
Location: Purdue University, Indiana, USA Join Date: Jun 2008
Posts: 1,104
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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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| Tags |
| bowtie, sequencing analysis, tophat bowtie |
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