metabarcoding sequences from Novogene which to use?

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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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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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