Finding the right greengenes files for training a classifier

[elaheahmadi (Elaheh Ahmadi)]

Dear Mehrbod
thank you for guide me I already read overview tutorial but With carelessness and I understand now. I have another question. I do Taxonomic analysis exactly matching with moving pictures tutorial but I use from --i-classifier Greengenes 13_8 99% OTUs full-length sequences and i dont use from Training feature classifiers with q2-feature-classifier. Are not my results accurate?
I wanted to use from trained taxonomic classifiers but i don’t find 99_otus.qza and 85_otu_taxonomy.txt in site for download just there is 85_otus.fasta in Training feature classifiers with the q2-feature-classifier page. and also about p-trunc-len in this section explain for me.
my primer is 27 f / 534 f from 16S gene.
please guide me.

[Mehrbod_Estaki]

Hi @elaheahmadi,
I've moved this post to a new topic as it was no longer related to the original thread topic. We ask that users keep their posts relevant to the original topic and new questions be posted as a new topic. Thanks for your understanding.

You'll want to train a classifier based on your specific primers instead of using the raw GG OTUs. This will significantly improve classifying your sequences, see this paper for more details.
Have you had a chance to read over the training classifier tutorial? This covers everything you'll need to know on how to train your classifier. Please go over it carefully. The data resource link provided there includes the complete greengene files, where for example if you download the 13_8 (most recent version) will have the 99_otus.fasta and 99_otu_taxonomy.txt in it. These are the 2 files you want to use, and not the 85 versions.
Also note that there are pre-trained classifiers also available so if your primers match the ones in that page or in the community resource category you can just use those instead of training your own.

@elaheahmadi

and also about p-trunc-len in this section explain for me.
my primer is 27 f / 534 f from 16S gene.

Please see the explanation in the tutorial and take care to also read the Note box regarding paired-end vs single end reads.

Good luck!