I'm analyzing a new dataset, and, after importing the data into Qiime2 I saw that the quality plot of my reverse reads drops to almost zero and, afterwards, increases.
I'm just wondering why this happened. When I denoise the data (using DADA2), should I trim the reverse reads necessarily up to 180 bp?
Yes, trimming at 180 would probably be your best option. Your second best option would be to contact your sequencing center, report this as a failed run, and ask them to run it again. It's possible (hopefully!) that this is some sort of software error and your run is OK, but if I saw that graph, I would see if they could rerun those samples.
Thanks for your feedback. I'm also including the forward plot for your analysis, and I did not see the same artifact with these reads. So, may I assume that this sequencing problem was limited to the reverse reads? Also, when I merge the reads and considering that to merge is only necessary a 20-bp overlap, by trimming the reverse reads up to 180 bp, would it be ok to proceed?
Thanks for your reply. I just included the forward plot as well. Do you think I can proceed analyzing this run, as I did not see the same artifact with the forward reads?