I have obtained 13,800 total features from 24 fecal microbiota samples of mice.
I would like to know if this number it is acceptable because until now both with qiime1 and qiime2 I have never had such a high number (I have obtained always around 2,000-4,000 ASVs/OTUs).
Yes, it's possible to get a lot of features from deep sequencing of a diverse community. If you ran any positive controls, you can use these to show reviewer three that you are not getting any extra OTUs.
Where any positive controls included on this run?
(I have seen barcodes end up as part of the amplicon sequence, and greatly increase feature count. This is another thing you could check with your positive controls, or with a PCoA plot. )
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