How can I merge outpus from qiime cutadapt demux-single?

Hi All,
I hope you are well! I have the following query, I was looking for how to join output files of 3 different analyzes done with qiime cutadapt demux-single:

I did not find how to do it. I would like to join the 3 files and then analyze them together in DADA2.
Thank you very much in advance!

Hi @PatoUru,
Are these 3 files from different sequencing runs or different primers/ PCR reactions? If so, you should denoise them separately with DADA2 and then merge them afterwards instead using the merging commands available here.

Hie @Mehrbod_Estaki
There are 3 different runs with the same primers.
I apologize if it is very basic what I ask you !! But, if I did three separate analyzes with DADA2 and then merge those 3 files, the ASV generated in each of the analyzes will have different names and it will not be possible to compare them?

1 Like

Hi @PatoUru,
No problem at all! Your questions are totally valid and not something you would have known on your own.
As long as you use the same trim/truncating parameters across all 3 runs then the ASVs produced will be comparable across the runs. The hashed ID produced for a specific ASV will always be the same. For example AATTGGCC will always give you the same ASV name regardless of which run it was from but AATTGGC will produce a completely different one. That’s why we have to use the same trimming across all 3 runs.

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