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?
Welcome to the 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
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
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
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?
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
Thank you for your reply, it well addressed the problem！