Training feature classifiers

[ptalebic (Pasha TC)]

Hi,

I am going to train my classifier. Based on this I need two elements: the reference sequences and the corresponding taxonomic classifications. I downloaded the reference sequences (Greengenes 13_8 most recent) from here

1- I was wondering where can I obtain the corresponding taxonomic classification. Can I use the one provided here?

2- The file I downloaded (Greengenes 13_8 most recent), after decompressing it I notice that there are many files in it. Which one should I use? Or I guess I should import it as a compressed file for traning my classifier?

Sorry for my silly questions

[andrewsanchez]

Hi, @ptalebic

Applying the workflow documented in Feature classifier tutorial can be a bit confusing at first. Luckily, there are already some discussions here on the forum about these points of confusion! Searching the forum for terms like "Greengenes" and "taxonomic classification" etc. will yield some helpful results:

Here are a few links with discussion relevant to your specific questions to get you started:

questions on the use of 16s greengenes database

Hi, everyone. I am Mavis, sorry to bother you, I really need some help. Today I want to generate taxonomy.qza with greengenes 16s database, and I downloaded the newest greengenes 16S rRNA database from the data resources page and chose the one named 13_8. I noticed the words which say before I use this, I need to import it into artifacts. So I unzip the gz file. However I can't see the unzipped file type from my computer . So my question is, what is the type of this file and what command sho…

Importing 13_8 Greengenes database for training classifier

Hi, I have a general question about importing the 13_8 Greengenes database into QIIME2 in order to train it as a classifier. I am using QIIME2 version 2019.1 on VirtualBox on a Mac. I clicked the link from the data resources page, and the resulting files are in my downloads as gg_13_8_otus.tar.gz and gg_3_8_otus.tar.gz.cpgz My question is what is the import command to import the database into QIIME? I've looked around the forum and at the training classifier/importing data pages, but I can't …

Best of luck!
Andrew