I got the following feature table after using DADA2... My supervisor would like me to subtract the feature counts of the Kit-Negative and PCR-Negative samples from all of the other samples and I was wondering if there was a plugin / method I can use to achieve this?
Hi @Doug_Szeto,
How to appropriately correct for contamination and handle negative controls is a really complciated topic that has been widely discussed here. Im going to refer you to this thread as a starting point, but the short answer is that you probably shouldn't, because it's not appropriate for the data.
Best,
Justine
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Would you recommend filtering out the Kit-Negative and PCR-Negative samples before moving onto form a phylogenetic tree for diversity analysis? Sorry if this is obvious, I'm new to all of this!
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Hi @Doug_Szeto,
These are good questions!
I tend to leave them in because I typically don't care about extra tips in my tree or taxonomic assignments. If the feature aren't present, QIIME will ignore them.
Depending on the biomass of your enviroment, you negative controls can be super important. A couple of good artilces you might like are
https://msystems.asm.org/content/3/3/e00218-17
and
https://msystems.asm.org/content/4/4/e00186-19/article-info
Which sort of talk about differences and contamination based on different enviroments. The short answer is if your enviroment is high biomass (most feces, oral, soil), your negative controls are of less importance than if you have a low or ultra low biomass enviroment (non-musosal tissues, neonates, built enviroment, etc).
Best,
Justine
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