Dear Mothur Group,
I have similar question like many others have in the forum.
I want to remove the singletons or say cutoff of 10 before running classify.otu and make.shared command. In order to do so I did following step.
From above command I got lots of output files named rare and abundant.
So my question is, if its okay to use either rare or abundant file as an input to make shared file and classify my OTU’s only based on rare or abundant.
But in biological world rare otu if it belongs pathogenic bacteria plays a crucial role and thus i am bit skeptical here.
At the same time singletons may give a very wrong picture of Diversity plots. So it would really kind if someone shed light on this topic to me.
Thanks and looking forward for replies!!