# How Do I Recover 18s Reads after Filtering in Qiime 2?

**URL:** https://forum.qiime2.org/t/how-do-i-recover-18s-reads-after-filtering-in-qiime-2/4205
**Category:** User Support
**Tags:** taxonomy, dada2, 16s, feature-table
**Created:** [May 17, 2018, 9:27pm UTC](https://forum.qiime2.org/t/how-do-i-recover-18s-reads-after-filtering-in-qiime-2/4205 "2018-05-17T21:27:50Z")
**Posts on this page:** 1
**Showing post:** 3

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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: [May 18, 2018, 3:36pm UTC](https://forum.qiime2.org/t/how-do-i-recover-18s-reads-after-filtering-in-qiime-2/4205/3 "2018-05-18T15:36:13Z")

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> [@AlfalfaResearcher](#):
>
> I am new to Qiime and to this forum, so I hope I am posting this in the right place

Welcome, you have definitely come to the right place 😄

> [@AlfalfaResearcher](#):
>
> Is there a way to make two separate taxonomies with one being only fungi and the other being only bacteria?

You have a couple different options, depending on whether you want to separate before or after taxonomy classification:

1. analyze together through taxonomy classification. Use the SILVA 16S + 18S database for classification (we have a pre-trained classifier for full-length SSU with this database, or you can train your own with your primers). Subsequently, you can split your sequences and feature tables into separate tables/sequences for bacteria/archaea and for eukaryota, or whatever taxonomic groups you are interested in, but using [qiime taxa filter-table](https://docs.qiime2.org/2018.4/tutorials/filtering/#taxonomy-based-filtering-of-tables-and-sequences).

2. After denoising/otu picking but prior to downstream steps (e.g., taxonomy classification) use [qiime quality-control exclude-seqs](https://docs.qiime2.org/2018.4/tutorials/quality-control/#excluding-sequences-by-alignment) to split your sequences into two different sets based on alignment to a reference sequence set (e.g., 18S sequences) within a certain percent similarity. I do not know what % similarity would be suitable for differentiating 16S and 18S sequences. If you know of a non-degenerate form of your primers (and primer sequences are included in your reads), or an internal sequence within your amplicon that easily differentiates 16S from 18S, you could use `exclude-seqs` with the `blastn-short` method, which is optimized for searching for very short sequence alignments, e.g, with a very high % similarity to differentiate these groups.

That should do it! I personally might go the former route, if there aren't concerns about the reference taxonomy, as it would be a little more streamlined and explicitly identify sequences that cannot be classified as 16S OR 18S. You could always use that approach to split seqs/tables, and then reclassify those sequences with a different reference database or taxonomy classifier if for some reason you suspect the 16S + 18S classifier would give inadequate results (I have no evidence that it would) or if you have a favorite database that you want to use.

I hope that helps!

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