How to get OTU or taxa level counts?

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1

Hello,

This is probably a simple answer but I can’t seem to find it. How do I see the number of OTUs per sample? And if I have a collapsed table on the family level, how can I see the number of families present in each sample?

Thanks!
Zach

2

Hello Zach,

For OTUs per sample, how about qiime feature-table summarize?
https://docs.qiime2.org/2018.6/plugins/available/feature-table/summarize/

That script might also work after you have collapsed your table at the family level.

Colin

3

Thanks for the reply, @colinbrislawn . When looking at table is the number of sequences you would use for rarefaction the number of OTUs?

4

Nope. Rarefaction performs random subsampling down to a specific number of reads per sample. So you would look at reads per sample, not OTUs per sample.

I think this user had a similar question to yours, and I think you may find our discussion helpful.

Let me know if that answers your question,
Colin

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5

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