I have 100 samples for 16s diversity. I have followed step from MiseqSOP.
When I run “make.shared(count=final.count_table)”, got error Your count file does not have group info, all reads will be assigned to mothurGroup.
And at the end of analysis I got OTUs and classification of OTUs , but did not get information how many OTUs per samples.
I suspect you may have accidentally left out the count table file at some point in the pipeline. Could you go back through the different versions of files ending in
count_table and use them as input to
count.groups? This should show you were you seem to be losing the count information. Once you narrow that down, let us know and we can figure out why you’re losing the information.
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