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Old 04-16-2020, 08:30 AM   #3
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Location: Rochester, NY

Join Date: Feb 2020
Posts: 7

I thought Phred+64 was no longer used for Illumina scores? I am pretty sure mine is encoded in Phred+33. And I specified qin=33 and qout=33 in the command.

The reason the threshold is 59 is not because it is Phred+64, but because the scores were increased during merging.
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