I just run some samples in a MiSeq following the Illumina workflow for preparing libraries. I decided to leave one well empty as negative control. Unfortunately I got some reads for that well.
I read that in that case is recommended to eliminate those sequences from the entire reads from all the samples. Is possible to do that with qiime2??
Removing features found in your negative control from all your other samples is NOT a good nor recommended idea anywhere I know. Partially because there is no way to know the source of that contamination and there is a very good chance that those are real feature in your other samples, probably dominant in nature too, therefore you would be throwing away correct, and meaningful features. The discussion of removing contaminants from this type of dataset is quite active in the literature at the moment and has been discussed on this forum extensively as well, I would recommend searching the forum a bit and reading some of those relevant threads for more details.
Good luck, it can be a tricky one for sure!
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