# Poor taxonomic resolution for ITS1 classification

**URL:** https://forum.qiime2.org/t/poor-taxonomic-resolution-for-its1-classification/25013
**Category:** User Support
**Tags:** taxonomy, feature-classifier
**Created:** [December 13, 2022, 6:32pm UTC](https://forum.qiime2.org/t/poor-taxonomic-resolution-for-its1-classification/25013 "2022-12-13T18:32:56Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![Antani](https://forum.qiime2.org/user_avatar/forum.qiime2.org/antani/32/11545_2.png) [@Antani](https://forum.qiime2.org/u/Antani)
#### Post date: [December 13, 2022, 6:32pm UTC](https://forum.qiime2.org/t/poor-taxonomic-resolution-for-its1-classification/25013/1 "2022-12-13T18:32:56Z")

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Hello,  
I am working on an ITS1 dataset and while I try to classify sequences I obtain a very poor classification.  
In fact \> 50% of my sequences are classified just at Kingdom level (Fungi).

Here is the pipeline I am using.

## IMPORT SEQS

qiime tools import   
--type 'SampleData[PairedEndSequencesWithQuality]'   
--input-path manifest.tsv   
--output-path reads.qza   
--input-format PairedEndFastqManifestPhred33V2

## DEMUX SUMMARISE

qiime demux summarize   
--i-data raw-reads.qza   
--o-visualization raw-reads.qzv

## DENOISING DADA2

qiime dada2 denoise-paired   
--i-demultiplexed-seqs raw-reads.qza   
--p-trunc-len-f 234   
--p-trunc-len-r 175   
--o-table table.qza   
--o-representative-sequences repseqs.qza   
--o-denoising-stats dada-stats.qza

## CLASSIFICATION

feature-classifier classify-sklearn   
--i-reads repseqs.qza   
--i-classifier unite\_classifier\_99\_27.10.2022.qza  
--o-classification taxonomy.qza   
--verbose

I was wondering if I am doing something wrong here.  
Can you help me improving my classification?

Thank you so much for your help!

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### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [December 13, 2022, 7:14pm UTC](https://forum.qiime2.org/t/poor-taxonomic-resolution-for-its1-classification/25013/2 "2022-12-13T19:14:24Z")

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Hi @Antani

If you search the forum you'll find several threads on this. The reason why so many taxa are only being classified as Fungi is because there are no outgroups in your reference set. That is, these sequences are likely non-fungal eukaryotes see, [here](https://forum.qiime2.org/t/classification-of-its-question/10113/11?), [here](https://forum.qiime2.org/t/building-a-database-in-order-to-train-a-classifier/15064/2?), and [here](https://forum.qiime2.org/t/suggestions-for-asv-table-with-its-fungi/17728/2?).

This issue crops up with other reference databases too, like [rRNA reference sequences](https://forum.qiime2.org/t/problem-with-taxa-summary-getting-to-many-k-bacteria/16010/5?).

I recommend using the unite database that also contains non-fungal eukaryotes.

-Mike

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [January 14, 2023, 1:14am UTC](https://forum.qiime2.org/t/poor-taxonomic-resolution-for-its1-classification/25013/3 "2023-01-14T01:14:43Z")

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