# DADA2\_Truncating both forward and reverse reads\_how?

**URL:** https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324
**Category:** User Support
**Tags:** dada2
**Created:** [March 6, 2018, 2:53pm UTC](https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324 "2018-03-06T14:53:08Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![Kruttika\_Phalnikar](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/k/eb8c5e/32.png) [@Kruttika\_Phalnikar](https://forum.qiime2.org/u/Kruttika_Phalnikar)
#### Post date: [March 6, 2018, 2:53pm UTC](https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324/1 "2018-03-06T14:53:08Z")

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Dear qiime community,

I am running dada2 for denoising my data

My qual visualization plots look like this

 ![Picture1](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/5/51ddab92d7d24e449487954510af1519b02e8df0.jpg)

I run the follwing command

qiime dada2 denoise-single   
--i-demultiplexed-seqs demux.qza   
--p-trim-left 0   
--p-trunc-len ()   
--o-representative-sequences rep-seqs-dada2.qza   
--o-table table-dada2.qza

now my forward reads are better than reverse and can be truncated after 245 position  
Reverse reads can be truncated after 190 position  
But I just have 1 option to put truncation value?  
If I put 190, do I lose good amount from forward reads?  
Is like I can't truncate both forward and reverse reads separately?

I tried using --p-trunc-len-f and --p-trunc-len-r  
qiime says it can't recognize these commands

I am refering to this discussion

> [@Truncating parameters on DADA2 (paired-end demultiplexed reads)](https://forum.qiime2.org/t/truncating-parameters-on-dada2-paired-end-demultiplexed-reads/2464):
>
> Hi, I am working with paired end reads that have been demultiplexed but have not undergone any other processing by the sequencing company (so primers/adapters are still attached). I imported using Phred33 manifest file. The graphs of the unjoined sequences are below: Based on [this comment](https://forum.qiime2.org/t/importing-fastq-gz-files-cassava-1-8/1748/17), I ran the following DADA2 command, using a smaller truncation parameter for the reverse reads based on the graph (Do I need to remove the primers/adapters first? I did not... I see fro…

in dada2 original tutorial, there is an option of truncating f and r separately before merging.

Could someone please explain?  
Thank you so much in advance

Kruttika

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### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [March 6, 2018, 3:35pm UTC](https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324/2 "2018-03-06T15:35:43Z")

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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: [March 6, 2018, 3:44pm UTC](https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324/3 "2018-03-06T15:44:56Z")

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Hi @Kruttika_Phalnikar,  
The issue is that you are using `qiime dada2 denoise-single`, but you should be using `qiime dada2 denoise-paired`. Check the [help docs](https://docs.qiime2.org/2018.2/plugins/available/dada2/denoise-paired/) — that method has the `--p-trunc-len-f` and `--p-trunc-len-r` parameters that you are looking for.

I hope that helps!

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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: [March 6, 2018, 3:44pm UTC](https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324/4 "2018-03-06T15:44:57Z")

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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: [April 6, 2018, 9:45pm UTC](https://forum.qiime2.org/t/dada2-truncating-both-forward-and-reverse-reads-how/3324/5 "2018-04-06T21:45:04Z")

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