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!
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.
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?
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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