What are the differences between two OTU tables

I used this commend to get a OTU table.

qiime diversity alpha \
–i-table table.qza
–p-metric observed_otus
–o-alpha-diversity observed_otus_vector.qza

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 :grinning:

Hi @Choe,

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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