Thank you @Vixer. Sorry if I am confused but, after processing my samples in FastaQ, I still have reads with the forward primer and other reads with the reverse primer both in R1 and R2 files for each sample. So the FastaQ Processor Mr DNA provides does not solve the issue of having both forward and reverse reads in R1 and R2 files. Am I right?
The fastaQ processor just give you the files to import into QIIME, they are still raw data. This is from their pipeline: To process the r1 and r2 files for amplicons <300bp.
a. MR DNA in this case now does attempt join the files we utilize the forward reads found in both r1 and r2 files. If you do not join the reads and utilize both the r1 and r2 by concatenating them or processing each in turn then all the barcodes do appear only in 5’-3’ orientation.
b. Perform quality trimming… keep all reads >250bp (subjective). And process as usual.
c. The same basic process is used by MR DNA for amplicons too long to be joined effectively.
tl;dr: you have to remove the primers by yourself. Luckily QIIME2 can do that with both dada2 and deblur. And all the primers are set in 5’-3’ orientation so you just need to specify the trimming leght (f and r) and that´s how you remove the primers.
After that, you can check the rep-seqs to see if your sequences still have the primers, which they are supposed not to by now.