Default phred score value for tophat2 and bowtie2

Question

[irritable_phd_syndrome]

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?

Answer 1

[Devon Ryan]

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.