DADA2 Merge problems

[ben (benjamin w.)]

Hi Shlomit, I was just troubleshooting samples for another group and these were roughly the recovery after DADA2. I think it's acceptable, but here's what I would do:

1. Check the quality of forward and reverse
2. Are these degenerate primers?

I found that the quality of overlap between the forward and reverse are likely the reason for many of these issues.

Please see this link where I was trouble shooting DADA2 V3V4 region:

Nextera paired-ends using a linker

Hi @ben, Definitely not a one-stop shop. There are many steps, each with its own troubleshooting peculiarities. We should really compile a single forum post to help navigate the process! Oh that's a tough one — I am not sure we have had to troubleshoot that step before, since usually filtering or merging is where the big issues happen. Maybe you could upload the qzv of your dada2 stats? Filtering has nothing to do with overlap — at that stage the reads are still being filtered independently…

I think after reviewing I had significant loss as well. Ben