Problem with demux

Hi @Nicholas_Bokulich,

Thank you so much for your answer!!

I have a follow-up question. I have just realized that the company attempts to join reads if the amplicon is longer than 300bp, which is not my case (I used 515F-806R). Given the length of my amplicon, would joining the fwd and reverse reads be of bad quality?

If this is the case, would it be better if I just analyze the data as single reads without joining them? Since the company provides a mixture of forward and reverse reads in each of the R1 and R2 files, how could I proceed? Should I reorient the reverse reads in both files, concatenate the files and remove primers and adaptors, then import them to qiime2 as single end sequences?

I guess my problem is the same as this one: Import multiplexed R1.fastq and R2.fastq with mixed forward and reverse reads + truncate reverse primer (although our amplicon sizes are different) and the same as the link you sent earlier. It seems we cannot import the files into qiime2 with PairEndSequences because we have fwd and rev reads in each of our R1 and R2.

Thank you so much for your help, I really appreciate your time!

L.