# Import merged fastq files via manifest

**URL:** https://forum.qiime2.org/t/import-merged-fastq-files-via-manifest/2930
**Category:** User Support
**Tags:** import
**Created:** [February 7, 2018, 5:20pm UTC](https://forum.qiime2.org/t/import-merged-fastq-files-via-manifest/2930 "2018-02-07T17:20:02Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![arwqiime](https://forum.qiime2.org/user_avatar/forum.qiime2.org/arwqiime/32/12728_2.png) [@arwqiime](https://forum.qiime2.org/u/arwqiime)
#### Post date: [February 7, 2018, 5:20pm UTC](https://forum.qiime2.org/t/import-merged-fastq-files-via-manifest/2930/1 "2018-02-07T17:20:03Z")

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Hello Qiime2 experts,  
I have a set of fastq.gz files of 50 environmental samples; they are already demultiplexed, primer-clipped and merged by BBmerge. I thought I should be able to import them using this procedure, but there are two points where I'm not sure whether I have used the correct specification (marked with ### below)

qiime tools import   
--type 'SampleData[SequencesWithQuality]' \ ### is this correct for fastq.gz files  
--input-path Manifest.csv   
--output-path import\_results.qza   
--source-format FastqGzFormat

Manifest.csv  
sample-id,absolute-filepath,direction  
sample-1,$PWD/some/filepath/sample1\_merged.fastq.gz,forward ### should it be 'forward' or 'merged'  
etc.

Thank you for your suggestions!  
Alfons

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### Author: ![Mehrbod\_Estaki](https://forum.qiime2.org/user_avatar/forum.qiime2.org/mehrbod_estaki/32/4001_2.png) [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)
#### Post date: [February 7, 2018, 6:37pm UTC](https://forum.qiime2.org/t/import-merged-fastq-files-via-manifest/2930/2 "2018-02-07T18:37:54Z")

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Hi @arwqiime,  
If you are planning on using dada2 in qiime2 it is better to import your reads unjoined as dada2 performs denoising on individual reads and then merges them. See this [thread](https://forum.qiime2.org/t/import-demultiplexed-joined-reads-r1-r2-joined/1356/3) where a similar question was discussed.  
If your plan is to use another method such as vsearch, I think this [tutorial](https://forum.qiime2.org/t/analyzing-paired-end-reads-in-qiime-2/2021/1) can help with your importing questions. Specific to your question, see the

> Importing pre-joined reads

section.

Hope that helps!

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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: [March 12, 2018, 7:32am UTC](https://forum.qiime2.org/t/import-merged-fastq-files-via-manifest/2930/5 "2018-03-12T07:32:24Z")

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