Question: Default phred score value for tophat2 and bowtie2
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4.7 years ago by
irritable_phd_syndrom70 wrote:

I have been looking at the bowtie2 and tophat2 manuals.  Tophat2 (which calls bowtie2) can be run without specifying a phred scoring.  In the documentation, it doesn't specify which is by default.  So which is it? 

bowtie tophat • 1.5k views
ADD COMMENTlink modified 4.7 years ago by Devon Ryan95k • written 4.7 years ago by irritable_phd_syndrom70
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gravatar for Devon Ryan
4.7 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

Phred+33. Everything should be assumed to take phred+33 by default unless explicitly stated otherwise, since that's all that's produced these days.

ADD COMMENTlink written 4.7 years ago by Devon Ryan95k
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