MOCK sample and PCR blanks

[thermokarst]

Hi @fstudart!

@fstudart

do I also have to remove the same sequences from rep-seqs.qza?

You could probably get away with not removing those features, but your phylogenetic tree will have some extra tips in it, which may or may not impact downstream analyses.

@fstudart

if so, is that possible

Yes! As I mentioned above, we now support this kind of filtering in QIIME 2 2017.9. Check out the docs for some more info on how to perform this, and let us know if you have any questions.

@fstudart

Because, I’ll use this file later on in the analysis to build the tree.

I would suggest trying building a tree and running your analyses both ways (with and without filtering), and see how the results compare, that way you can be confident you are making the right decision.

Thanks!