# poor classification using qiime2
**URL:** https://forum.qiime2.org/t/poor-classification-using-qiime2/25962
**Category:** User Support
**Tags:** feature-classifier
**Created:** [March 29, 2023, 10:44am UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962 "2023-03-29T10:44:00Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@MichelaRiba](https://forum.qiime2.org/u/MichelaRiba)
#### Post date: [March 29, 2023, 10:44am UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/1 "2023-03-29T10:44:00Z")
Good morning,
I am experiencing some difficultie sto get results even if indeed my pipeline has not changed.
In specific what I obtain is kind of poor classification: half of the sequences (very low number of OTU in addition (e.g 900) are just attributed to Bacteria or OD1. So I think this is not a great result.
I include my commands
taxa\_classi:
$(CONDA\_ACTIVATE) Miqiime2-2021.8;
qiime feature-classifier classify-sklearn
--i-classifier gg-13-8-99-nb-classifier.qza
--i-reads **rep-seqs-or-85.qza**
--o-classification taxonomy10C.qza
joined\_import\_filter\_derep:
export HDF5\_USE\_FILE\_LOCKING='FALSE';
$(CONDA\_ACTIVATE) Miqiime2-2021.8;
qiime vsearch dereplicate-sequences
--i-sequences fil\_joined.qza
--o-dereplicated-table table.qza
--o-dereplicated-sequences **rep-seqs.qza**
Couls you please help me?
Thanks a lot
I specify I did not check at the moment if primers for sequencing have changed or so
Michela
I would appr4ciate very much you kind help.
---
### Author:  [@crusher083](https://forum.qiime2.org/u/crusher083)
#### Post date: [March 29, 2023, 11:07am UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/2 "2023-03-29T11:07:47Z")
Hello Michela,
The information about primers would be crucial. It is the most possible explanation for the poor performance of the classifier.
Cheers
Valentyn
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### Author:  [@MichelaRiba](https://forum.qiime2.org/u/MichelaRiba)
#### Post date: [March 29, 2023, 11:46am UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/3 "2023-03-29T11:46:35Z")
Hi Valentyn, I will be back with information about primers, for sure I would need indications on waht classifier would be best fitted.
Thanks a lot for you support
Michela
---
### Author:  [@crusher083](https://forum.qiime2.org/u/crusher083)
#### Post date: [March 29, 2023, 12:00pm UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/4 "2023-03-29T12:00:19Z")
After you obtain primer sequences you can refer to a tutorial on building a reference database here:
> [@Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494):
>
> construction Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt [RESCRIPt](https://github.com/bokulich-lab/RESCRIPt) (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…
Cheers
Valentyn
---
### Author:  [@MichelaRiba](https://forum.qiime2.org/u/MichelaRiba)
#### Post date: [March 29, 2023, 12:13pm UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/5 "2023-03-29T12:13:37Z")
Thanks a lot!
could you please remind me of which primers are compatible with this classifier database
gg-13-8-99-nb-classifier.qza
?
This will help me very much to recontruct the sudden impossibility of classification starting from the same facility.
I would appreciate it very much
Michela
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [March 29, 2023, 10:29pm UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/6 "2023-03-29T22:29:47Z")
More details are avaiable on the [data resources page](https://docs.qiime2.org/2023.2/data-resources/).
> Naive Bayes classifiers trained on:
>
> - [Greengenes 13\_8 99% OTUs full-length sequences](https://data.qiime2.org/2022.11/common/gg-13-8-99-nb-classifier.qza) (MD5: `6bbc9b3f2f9b51d663063a7979dd95f1`)
> - [Greengenes 13\_8 99% OTUs from 515F/806R region of sequences](https://data.qiime2.org/2022.11/common/gg-13-8-99-515-806-nb-classifier.qza) (MD5: `9e82e8969303b3a86ac941ceafeeac86`)
`gg-13-8-99-nb-classifier.qza` is the first one. So, no primers are used to select a region _at all_ so the full 16S region is used for k-mer profiling and classification.
Using RESCRIPt to build a database for just your region of interest should perform better because it's more specific.
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 30, 2023, 4:30am UTC](https://forum.qiime2.org/t/poor-classification-using-qiime2/25962/7 "2023-04-30T04:30:21Z")
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