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Forum: Bioinformatics 09-14-2011, 12:33 PM
Replies: 1
Views: 1,916
Posted By zhenhua
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...
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