Normalization to the group with lowest sequence count is demonstrated as a must, however, if one of the samples has a low count (in my case 160 seqs), how can i remove those samples or groups.
here how i did it but not sure if it is the most efficient way:
i went back to files prior to OTU analysis i.e.
and removed the unwanted groups:
remove.groups(fasta=final.fasta, name=final.names, group=final.groups, taxonomy=final.taxonomy, groups=G2-G3-G6-G7)
Removed 6281 sequences from your name file. Removed 2530 sequences from your fasta file. Removed 6281 sequences from your group file. Removed 2530 sequences from your taxonomy file.
Output File names:
then i redid the dist.seqs, cluster, make.shared, and count.groups and finally finishing with sub.samples.
Is this the correct or best way, since re"cluster"ing takes lots of time.