What are the differences between two OTU tables

User Support
1

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:

3

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!