Multi-gene amplicon sequences with dada2

[DimitraIoli]

Hi! I have demultiplexed sequences for eukaryotes (18S) and bacteria (16S) in the same fasta file. I would like to analyze only the sequences for bacteria. I was wondering if I should separate them before running dada2. If yes how I can do that? Otherwise, can I proceed without separating the two different amplicons by setting the appropriate parameters in filterAndTrim? Thanks, Ioli

[benjjneb]

I was wondering if I should separate them before running dada2.

It isn't necessary. You can run the data with both 16S + 18S sequences in it through DADA2 as per normal, and will get a mix of 16S/18S ASVs in the end pretty much as normal.

Otherwise, can I proceed without separating the two different amplicons by setting the appropriate parameters in filterAndTrim?

If your focus is on the bacterial sequences, make sure that your filterAndTrim parameters are appropriate for the bacterial 16S amplicon, e.g. removing the primers correctly and keeping overlap in paired-end data.

[DimitraIoli]

Hi Benjamin! Thank you for your reply. Cheers, Ioli