Default phred score value for tophat2 and bowtie2
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?
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Ram
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irritable_phd_syndrome •
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irritable_phd_syndrome •
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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.
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Devon Ryan
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