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Old 11-07-2016, 01:58 PM   #3
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 823
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I'd suggest looking for contamination in that sample (e.g. using BLAST to find out what the most abundant read maps to).

At least three replicates should be used to determine which (if any) samples are outliers. If you've found an outlier, and have another reason to exclude it, then it would be reasonable to exclude that sample from the analysis. Ideally, you would do another library prep and sequencing to make up the numbers, but people tend to dislike spending more money for statistical robustness.
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