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Old 04-22-2020, 01:38 PM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080

Yikes this is a really low diversity sample. Do you know how much phiX (if any) was added to this sample. Did you not tell the sequence provider that these were low diversity? If you did not then it would be hard to make a case for them to re-sequence this sample again for free. You may have to pay for a re-run with a significant % of phiX (10-20% or more), if you want to get improved Q-scores.

It is possible that in spite of the bad Q-scores etc your sequence may still be usable. Have you looked at that?
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