I have a doubt
I have some raw sequences that are already demultiplexed but still have its adapters. Is the adapters are same as barcodes? which plugin shall I use for removing the adapters? I do not have any information about the sequences of the adapters.
How can I get rid of the adapters in my raw sequences after I import them and before performing DADA2?
Barcodes are used to identify which sample a sequence is from, adapters (in the Illumina world) are sequences used to to attach the sequence fragments to the plate so that they can be read. You will need reach out to your sequencing center to find out which adapters were used, as this depends on the particular protocol used by the center.
Once you know which adapters were used, you can remove them with q2-cutadapt or with DADA2.
q2-cutadapt offers many options while DADA2 is a bit limited but often a very convenient option. Check out this doc for more information.
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