# Fungal ITS sequence from Illumina returns many unclassified reads **URL:** https://forum.qiime2.org/t/fungal-its-sequence-from-illumina-returns-many-unclassified-reads/20864 **Category:** User Support **Tags:** taxonomy, feature-classifier, fungi **Created:** [September 23, 2021, 9:58pm UTC](https://forum.qiime2.org/t/fungal-its-sequence-from-illumina-returns-many-unclassified-reads/20864 "2021-09-23T21:58:06Z") **Posts on this page:** 1 **Showing post:** 2
### 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: [September 24, 2021, 9:21pm UTC](https://forum.qiime2.org/t/fungal-its-sequence-from-illumina-returns-many-unclassified-reads/20864/2 "2021-09-24T21:21:17Z")
Hi @linjie_0911, Not sure why you are using SILVA for ITS reads. SILVA _only_ contains sequence data for SSU rRNA genes (i.e. 16S & 18S). So, I would not trust any classifications of ITS data resulting from a search against the SILVA db. Could you provide more details on what primer sets you used? Did you merge paired-end reads, or just use the forward read? For example see this post of helpful questions: > [@Fungal ITS classification with UNITE database](https://forum.qiime2.org/t/fungal-its-classification-with-unite-database/2003/4): > > Hi @Hillary_Smith, Thanks for posting! And many thanks for checking out the other forum posts related to this issue first. I have a few questions to get started troubleshooting: What primers are you using? What is the length of the sequences that you are classifying? What types of samples are you analyzing? (just curious but it may be relevant here) One way to test your classifier would be to classify a subset (10 would be enough) of the same sequences that you used to train the classifier. … Perhaps provide a list of commands, or simply the QZV file of the taxonomy barplot so we can look at the provenance information. Feel free to DM me if you do not want to share publicly. Finally, if you search the forum you'll come across quite a few threads about Fungal ITS analysis. Here is one to get you started: > [@Fungal ITS analysis tutorial](https://forum.qiime2.org/t/fungal-its-analysis-tutorial/7351): > > Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a [QIIME 2 workshop](https://workshops.qiime2.org/microbiome-bioinformatics-qiime-2-2018-12-12/) in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the [q2-itsxpress tutorial](https://forum.qiime2.org/t/q2-itsxpress-a-tutorial-on-a-qiime-2-plugin-to-trim-its-sequences/5780) for other fungal ITS analysis options in QII… -Cheers! --- _[View the full topic](https://forum.qiime2.org/t/fungal-its-sequence-from-illumina-returns-many-unclassified-reads/20864)._