I have AOA sequence from Illumina with 250 reads technique. Actually, AOA is around 632 bp, so R1 and R2 will not have any overlap
Can I use Qiime2 (dada2) to join R1 and R2 or not?
if not, which one can I use for this analysis
Thank you very much
I was under the impression that DADA2 requires at a minimum 20 NT overlap between the forward and reverse reads. But I believe that the developers occasionally frequent this site. Ben
Have a look at this thread with a similar question. The short answer is no, q2-dada2 cannot merge without overlaps (the min overlap for q2-dada2 USED to be 20, but now is 12). In native version of dada2 in R there is an option to concatenate non-merging reads by inserting 10 N in-between, but again, do you really trust those reads? I wouldn’t…my recommendation is to just use your forward reads that generally are in better shape.