How could I combined featuure table and taxamony for Enterotype identification?

Hello. I am now working on 16s rRNA analysis. And I get ASVs table and taxamony for my sample, then how could I combined featuure table and taxamony for Enterotype identification? I try to use qiime taxa collapse but I'm not sure. Maybe i need relative frequencies table. Is there any way to do that?

Hi @Duyh814,

Welcome to the :qiime2: forum!

It sounds like qiime taxa collapse is what you want! It will give you a feature table but it will collapse all the asv so they are labeled to the taxonomic level that you specific .

Can you explain what you mean by Enterotype identification? that would allow me to better understand what your goals are!

Hope that helps
:turtle:

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Thanks for your reply ll .Enterotype means clustered sample using JSD distance metric based on the relative abundances of bacteria at the genus level. So i wonder if there anyway to get a relative abundances ASVS. l tried qiime ''feature-table relative-frequency'' but it can not convert result of qiime taxa collapse to relative avybdabce

Hi @Duyh814,

I think you found the command that will do what you want.

Can you post the error you are receiving for this? You absolutely should be able to convert a collapsed table to relative frequency. However, you will not be able to collapse a relative frequency table so make sure you are runing the commands in the correct order:

qiime taxa collapse 

qiime feature-table relative-frequency 

Hi @cherman2
Thanks a lot.
I use the follow command

qiime feature-table relative-frequency --i-table table-or-97.qza --o-relative-frequency-table table-or-97-relative.qza
 time qiime taxa collapse  --i-table table-or-97-relative.qza  --i-taxonomy taxonomy.qza --p-level 6 --o-collapsed-table or-97-table-l6-relative.qza

and I got a error: (1/1) Invalid value for '--i-table': Expected an artifact of at least type FeatureTable[Frequency]. An artifact of type FeatureTable**[RelativeFrequency]** was provided.

the result of qiime feature-table relative-frequency is type [RelativeFrequency], qiime taxa collapse can not solve it. Is there any other way, or do I need to do the matching myself?

Best.

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Hi @Duyh814,
You need to collapse your feature table and then run relative frequency. You can not run relative frequency then taxa collapse you will get the error that you are receiving:

(1/1) Invalid value for '--i-table': Expected an artifact of at least type FeatureTable[Frequency]. An artifact of type FeatureTable**[RelativeFrequency]** was provided.

This should be the order of the commands:

qiime taxa collapse  --i-table table-or-97.qza  --i-taxonomy taxonomy.qza --p-level 6 --o-collapsed-table or-97-table-l6.qza

qiime feature-table relative-frequency --i-table or-97-table-l6.qza --o-relative-frequency-table or-97-table-l6-relative.qza
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Thank you for your reply, it well addressed the problem!

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