# metabarcoding sequences from Novogene which to use?

**URL:** https://forum.qiime2.org/t/metabarcoding-sequences-from-novogene-which-to-use/32249
**Category:** User Support
**Tags:** import
**Created:** [January 7, 2025, 12:03am UTC](https://forum.qiime2.org/t/metabarcoding-sequences-from-novogene-which-to-use/32249 "2025-01-07T00:03:07Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![kevin\_SalOrt](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kevin_salort/32/12999_2.png) [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)
#### Post date: [January 7, 2025, 12:03am UTC](https://forum.qiime2.org/t/metabarcoding-sequences-from-novogene-which-to-use/32249/1 "2025-01-07T00:03:07Z")

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Hi buddies.  
I´m doing some 16S metabarcoding experiments. I got my metabarcoding sequences from Novogene and they sent me 3 type files:  
\*.extendedFrags.fastq.gz (reads after merging)  
\*\_1.fastq.gz (reads with barcode and primer removing)

- raw\_1.fastq.gz (reads with barcode and primer)

as i know (by previous experiece, working with sequences from Macrogene) i used to import my raw sequences, but these reads from Novogene makes me some noise.  
What might happen if i import extendedfrags reads? I migh get similar ASVs like if i were made them from raw ones?

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### Author: ![colinvwood](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinvwood/32/17303_2.png) [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [January 7, 2025, 12:16am UTC](https://forum.qiime2.org/t/metabarcoding-sequences-from-novogene-which-to-use/32249/2 "2025-01-07T00:16:04Z")

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Hello @kevin_SalOrt,

If you plan to use dada2 to denoise & dereplicate your reads then it would be highly preferable to import the unmerged reads and let dada2 handle the merging. If you do not plan to use dada2 then I believe importing pre-merged reads will not be an issue

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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: [February 7, 2025, 6:16am UTC](https://forum.qiime2.org/t/metabarcoding-sequences-from-novogene-which-to-use/32249/3 "2025-02-07T06:16:43Z")

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