Combined ITS and 16s classifier


#1

Hello!

I have a dataset that I would like to analyse with both gg-13-8-99-515-806-nb-classifier.qza and unite-ver7-99-classifier-20.11.2016.qza. I was wondering if it was possible to do this all at once and create a single taxonomy file with all of this data present in it.

What Im hoping to do is create a correlation analysis where I can see how the bacterial levels change in response to fungal species present.

Thanks so much!! qiime is the best!

Scott


(Colin Brislawn) #2

Hello Scott,

I suppose this might be possible by retraining your own classifier using both 16S and ITS reads. After all, you can train silva to run on both 16S and 18S amplicons. But I think there is a more elegant and arguably more defensible option: process them separately, then merge your OTU tables.

qiime feature-table merge \
  --i-tables table-1.qza \
  --i-tables table-2.qza \
  --o-merged-table table.qza

Warning! :stop_sign: This only works if all your OTUs have different names. You wouldn’t want 16S OTU_1 and ITS OTU_1 to be added together! So after you merge, do a quick qiime feature-table summarize to make sure that all your OTUs from both data sets are present and combined number of OTUs didn’t go down after the merge.

While I’m mentioning this, you might want to think about methods for normalizing between the two different amplicon types (but that might not be a big issue if all your changes are relative :man_shrugging: ).

Let me know what method you want to try.
Colin


#3

Thanks so much for the info! I will try to merge the tables, all the OTUs should have different names. This is a great idea!

Thanks again, Ill let you know how it goes!

Scott