Keeping OTUs/ASVs with filter.shared


I have samples from different environmental locations. One of the locations has 1 exclusive ASV that is very abundant in that specific location. However, when I clean the data with the filter.shared command, it eliminates this ASV because it is only present in 6 out of 62 samples. Is there a way to tell mothur to keep specific ASVs/OTUs? In advance, thank you for your help.


Hi - I generally am not a fan of “filtering” shared files (in spite of hte fact that we have the command). If you want to do something like this, you will need to do something custom in R or elsewhere.


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