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Old 03-15-2012, 11:39 AM   #2
CS Student
Location: US

Join Date: Apr 2011
Posts: 20

I was able to solve this issue using the following two options:

1. --qv-offset 64: Interpret qvs in fastq input as PHRED+<value>. The default is 33 for colour space and 64 for letter space.

2. --ignore-qvs: When input is fastq, completely ignore base/colour qvs from the analysis, as if the input were fasta.
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