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Old 12-10-2018, 02:59 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,062

If samples are truly absent then you may not get any reads assigned to them as long as your libraries are excellent quality and run has worked well.

That said if you allow errors during demultiplexing you may start seeing some reads getting assigned to the phantom samples. If that number is negligible then you can ignore those samples but if they start becoming significant you may have to go back and examine how your sample pools are being made (I assume they are being individually made independently?) and if there are any problems there.
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