# How to change the paired-end-demux.qza into single-end-demux.qza(containing only forward reads)

**URL:** https://forum.qiime2.org/t/how-to-change-the-paired-end-demux-qza-into-single-end-demux-qza-containing-only-forward-reads/18481
**Category:** Ideas and Suggestions
**Tags:** demux
**Created:** [February 13, 2021, 2:59pm UTC](https://forum.qiime2.org/t/how-to-change-the-paired-end-demux-qza-into-single-end-demux-qza-containing-only-forward-reads/18481 "2021-02-13T14:59:09Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![HeinzG](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/58f4c7/32.png) [@HeinzG](https://forum.qiime2.org/u/HeinzG)
#### Post date: [February 13, 2021, 2:59pm UTC](https://forum.qiime2.org/t/how-to-change-the-paired-end-demux-qza-into-single-end-demux-qza-containing-only-forward-reads/18481/1 "2021-02-13T14:59:09Z")

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Hi,

I got a paired-end-demux.qza from paired reads using the following command:  
qiime tools import   
--type 'SampleData[PairedEndSequencesWithQuality]'   
--input-path manifest.tsv   
--output-path Sr\_paired\_end-demux.qza   
--input-format PairedEndFastqManifestPhred33V2

However, I found the reverse reads had a very low-quality scores. So I plan to use the forward reads for further analysis. Is there any method changing the paired-end-demux.qza into single-end-demux.qza containing only forward reads directly, rather than importing the forward reads again using SingleSequencesWithQuality?

Thank you!

Guo

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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: [February 15, 2021, 7:06am UTC](https://forum.qiime2.org/t/how-to-change-the-paired-end-demux-qza-into-single-end-demux-qza-containing-only-forward-reads/18481/2 "2021-02-15T07:06:33Z")

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> [@HeinzG](#):
>
> Is there any method changing the paired-end-demux.qza into single-end-demux.qza containing only forward reads directly, rather than importing the forward reads again using SingleSequencesWithQuality?

I have good news: Yes!

Both denoising methods in QIIME 2 can accept single-end or paired-end reads... and the following methods will ignore the reverse read if it is provided:

- **`qiime deblur denoise-16S`** (this method is intended for single-end or pre-joined reads, and so if paired-end reads are given only the forward reads are used)
- **`qiime dada2 denoise-single`** (this method is intended for single-end reads. The separate `denoise-paired` method denoises paired-end reads, but `denoise-single` just ignores the reverse reads if they are provided)

So you do not need to do anything — just select one of the methods above for denoising and the reverse reads in your `SampleData[PairedEndSequencesWithQuality]` artifact will be silently ignored.

Good luck!

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### Author: ![HeinzG](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/58f4c7/32.png) [@HeinzG](https://forum.qiime2.org/u/HeinzG)
#### Post date: [February 16, 2021, 9:26am UTC](https://forum.qiime2.org/t/how-to-change-the-paired-end-demux-qza-into-single-end-demux-qza-containing-only-forward-reads/18481/3 "2021-02-16T09:26:11Z")

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Good news to me. Thank you!