# Truncate length for V3-V4 sequencing in dada2 process

**URL:** https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539
**Category:** Technical Support
**Tags:** feature-classifier, dada2, demux, truncate, relative-frequency, primers, feature-table
**Created:** [March 23, 2022, 10:05am UTC](https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539 "2022-03-23T10:05:59Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![Muhammad\_Zeeshan\_Akr](https://forum.qiime2.org/user_avatar/forum.qiime2.org/muhammad_zeeshan_akr/32/13014_2.png) [@Muhammad\_Zeeshan\_Akr](https://forum.qiime2.org/u/Muhammad_Zeeshan_Akr)
#### Post date: [March 23, 2022, 10:05am UTC](https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539/1 "2022-03-23T10:05:59Z")

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Hi all, sorry for this question, i know it might have asked so many times. I just want to get more insights into it. Please provide your inputs. Thanks in advance.

I have sequencing data (2​✖300) of V3-V4 regions. This is a look of my fastq files which includes 2 index sequences in the header. Is there any need to remove these sequences.

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/1/1189a20111d2deaaa23f14f8179b2affcc778512.png)

When i denoised it using these parameters, i found very weird results.  
Truncate length of forward: 220  
Truncate length of reverse: 190  
I selected these length based on quality of reads.

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/1/196e9f390eb8541a543de318d4adcb1c15355354.png)

After denoising, i got very few number of features and frequencies.

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/d/d3eabe11c8f5d77d143aea6b36067ac3eb56c81c.png)

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/9/98da93e2cc6b92978b1ee69da1be29cb439f1151.png)

The stat table is showing i have enough number of reads but not merged and non-chimeric reads. There is a problem with merging of forward and reverse reads. I think forward and reverse read are not overlapping properly. Could you please input your suggestions, what should i do to resolve this issue. What should be the length of forward and reverse read for enough overlapping.

regards  
Muhammad

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### Author: ![timanix](https://forum.qiime2.org/user_avatar/forum.qiime2.org/timanix/32/17879_2.png) [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [March 23, 2022, 12:10pm UTC](https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539/2 "2022-03-23T12:10:17Z")

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3 off-topic replies have been merged into an existing topic: [Casava files of paired end reads](https://forum.qiime2.org/t/casava-files-of-paired-end-reads/22527)

Please keep replies on-topic in the future.

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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 23, 2022, 6:10pm UTC](https://forum.qiime2.org/t/truncate-length-for-v3-v4-sequencing-in-dada2-process/22539/3 "2022-04-23T18:10:34Z")

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