# Importing Merged\_Reads.fq into Qiime2 pipeline

**URL:** https://forum.qiime2.org/t/importing-merged-reads-fq-into-qiime2-pipeline/26683
**Category:** User Support
**Tags:** import
**Created:** [June 2, 2023, 11:41pm UTC](https://forum.qiime2.org/t/importing-merged-reads-fq-into-qiime2-pipeline/26683 "2023-06-02T23:41:38Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![rr220](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/r/45deac/32.png) [@rr220](https://forum.qiime2.org/u/rr220)
#### Post date: [June 2, 2023, 11:41pm UTC](https://forum.qiime2.org/t/importing-merged-reads-fq-into-qiime2-pipeline/26683/1 "2023-06-02T23:41:38Z")

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Hello,

I need help with a import command for merged\_reads.fq  
The sequencing center has not provided individual fastq files for analysis. They sent data as merged\_reads.fq format. How do I import this into qiime?

Usually I create raw reads folder that contains FASTQ files for each sample and then use this command:  
qiime tools import   
--type 'SampleData[PairedEndSequencesWithQuality]'   
--input-path   
--input-format CasavaOneEightSingleLanePerSampleDirFmt   
--output-path demux-paired-end.qza

How should I edit the above command for merged\_reads.fq?

I would appreciate your help.

Thank you,  
Best,  
R

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### Author: ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [June 5, 2023, 3:31pm UTC](https://forum.qiime2.org/t/importing-merged-reads-fq-into-qiime2-pipeline/26683/2 "2023-06-05T15:31:48Z")

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Hi @rr220,

Good question! Here's a really helpful answer from @cherman2 regarding importing pre-merged sequences, along with some resources for performing quality control on your data:

> [@Importing alreday merged reads](https://forum.qiime2.org/t/importing-alreday-merged-reads/19015/2):
>
> Hello @NH_20, Welcome to the QIIME2 Community! :qiime2: [Here](https://docs.qiime2.org/2021.2/tutorials/read-joining/#importing-pre-joined-reads) is a tutorial to import pre-merged data. I hope this helps you import your data. [Here](https://forum.qiime2.org/t/can-dada2-be-carried-on-pre-joined-reads/7269/5) and [here](https://forum.qiime2.org/t/import-demultiplexed-joined-reads-r1-r2-joined/1356) are discussions for how to do quality control with pre-merged reads. If you are unsure how to run quality control commands discussed in those links, I would recommend [this section](https://docs.qiime2.org/2019.10/tutorials/moving-pictures/#sequence-quality-control-and-feature-table-construction) of the moving pictures tutorial. I hope this helps! Chloe turtle

Hope this helps! Cheers 🦎

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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: [July 6, 2023, 9:31pm UTC](https://forum.qiime2.org/t/importing-merged-reads-fq-into-qiime2-pipeline/26683/3 "2023-07-06T21:31:49Z")

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