I used this commend to get a OTU table.
qiime diversity alpha \
But I just realized that there was a
observed_otus_vector.qza file in
core-metrics-results folder as well.
I expected that those two files showed same value, but it didn’t.
What are the differences between those two OTU tables?
Thanks in advance
The difference between these two outputs is likely due to the fact that in
core-metrics you are required to provide a sampling depth which all the reads are rarefied to. Where with
diversity-alpha no rarefying has been done. If you were to rarefy your table first to the same depth as the
core-metrics approach, you should get the same result. Hope that helps!
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