Adding 'N' when merging Forward and Reverse reads

[barakdror]

Hi,

i hope I didn’t missed any topic about it, but I couldn’t find an answer:
i have both Forward and Reverse fasta files of my samples. Is there a way, when demtiliplexing
the reads, to merge the F and R files and add a fixed number of ‘N’ between them?
i’ll elaborate- I did an amplicon sequencing for a 700bp fragment. However my F and R reads are around 280-300 each bp each, so I want to merge them and add 100 'N’s between the R and F.
Is that possible using qiime2?

Thanks a lot,
Barak

[Nicholas_Bokulich]

I did an amplicon sequencing for a 700bp fragment. However my F and R reads are around 280-300 each bp each, so I want to merge them and add 100 'N’s between the R and F.

Is that possible using qiime2?

No, that is not currently possible using QIIME 2. You will need to join these reads externally using a separate tool and then import to QIIME 2.

I do not know how this would impact downstream analyses, but would worry how OTU picking and taxonomy classification would be impacted. Denoising would not be possible if you insert Ns like this.

Good luck!