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Old 08-29-2013, 07:01 AM   #25
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Join Date: Mar 2013
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Originally Posted by maubp View Post
Yes, although in this case you could use PHRED quality 0 (and I recall some tools may use the upper bound 93 as a special value).
Thanks. I take it the encoding of missing values depends on the sequencer and it cannot be changed downstream. Therefore, I don't see how some downstream tool can use 93 as a missing value when it is not seen as such by the sequencing instrument.
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