I want to know what people who have used fastx or similar have done to define a poor quality read. What do you call a bad base (I was thinking of calling one bad if it had a score of 20 or below from phred33) and how many bad bases do you allow per read? I wondered if >=1 bad Base per 10 would definite a bad read. So if I had a 100 bp read, 10 or more bases with a score or 20 or less would be rejected. Does this sound right? Too strict? To relaxed?
Thanks for any advice
Thanks for any advice
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