# Quick clarification on feature classifiers

**URL:** https://forum.qiime2.org/t/quick-clarification-on-feature-classifiers/10206
**Category:** General Discussion
**Created:** [June 12, 2019, 11:39pm UTC](https://forum.qiime2.org/t/quick-clarification-on-feature-classifiers/10206 "2019-06-12T23:39:11Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![ctekellogg](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ctekellogg/32/5742_2.png) [@ctekellogg](https://forum.qiime2.org/u/ctekellogg)
#### Post date: [June 12, 2019, 11:39pm UTC](https://forum.qiime2.org/t/quick-clarification-on-feature-classifiers/10206/1 "2019-06-12T23:39:11Z")

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Hi there,  
I have a (hopefully) quick question regarding the current feature classifiers and how they compare to the blast from QIIME v 1.9, for example. I am turning back to an old, partially analyzed 16S/18S V6-V8 dataset and want to update the classifications to use the newest version of Silva. Previously, I classified my OTUs using Blast in QIIME 1.9. I thought I'd use the new classifiers from QIIME2 when updating the classifications and noticed that each of them (vsearch, consensus-blast+ and the naive-bayes classifier) yield lower taxonomic resolution than when I classified in QIIME1. I read this post: [Feature-classifier with Blast reference dataset](https://forum.qiime2.org/t/feature-classifier-with-blast-reference-dataset/4891) and it leads me to believe that since they are consensus based, rather than top hit based (as the old QIIME1 version of blast was...correct?), that the newer classifiers yield a more conservative ID, thus the lower taxonomic resolution. And then, I cross-checked a few where the resolution was really low compared to my old ID by running them through the Silva classifier online ([Alignment, Classification and Tree Service](https://www.arb-silva.de/aligner/)) and that classified them to quite a bit higher taxonomic resolution as well; so is this again a case of "top hit" vs. consensus. Just wondering what I should trust or go with for my final IDs! If anyone has any opinions or advice, I'd greatly appreciate it! Maybe I just need to adjust the settings in the new classifiers a bit to approach the IDs that I got during my last go-around in QIIME1.9. Or maybe I should just stick with this conservative IDs, as that is better....

Thank you in advance for your input!  
Colleen

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [June 13, 2019, 5:46am UTC](https://forum.qiime2.org/t/quick-clarification-on-feature-classifiers/10206/2 "2019-06-13T05:46:46Z")

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Hi @ctekellogg,  
Good questions!

> [@ctekellogg](#):
>
> it leads me to believe that since they are consensus based, rather than top hit based (as the old QIIME1 version of blast was…correct?), that the newer classifiers yield a more conservative ID, thus the lower taxonomic resolution.

correct

> [@ctekellogg](#):
>
> I cross-checked a few where the resolution was really low compared to my old ID by running them through the Silva classifier online ([Alignment, Classification and Tree Service](https://www.arb-silva.de/aligner/)) and that classified them to quite a bit higher taxonomic resolution as well; so is this again a case of “top hit” vs. consensus.

yes (to my knowledge)

> [@ctekellogg](#):
>
> Just wondering what I should trust

trust us!

> [@ctekellogg](#):
>
> Maybe I just need to adjust the settings in the new classifiers a bit to approach the IDs that I got during my last go-around in QIIME1.9.

you could set `maxaccepts=1` to do that... but then it is top hit and totally inaccurate!

> [@ctekellogg](#):
>
> Or maybe I should just stick with this conservative IDs, as that is better…

if it is too conservative we can help... check out the [paper](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0470-z) for recommendations. But overall you should use the consensus classifiers to avoid dire misclassifications.

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### Author: ![ctekellogg](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ctekellogg/32/5742_2.png) [@ctekellogg](https://forum.qiime2.org/u/ctekellogg)
#### Post date: [June 18, 2019, 5:22pm UTC](https://forum.qiime2.org/t/quick-clarification-on-feature-classifiers/10206/3 "2019-06-18T17:22:25Z")

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Hi @Nicholas_Bokulich - Thank you so much for your response and clarifications. I'll look back over the paper you've provided a link to as well and let you know if I have any further questions.

Colleen
