I recently got some data back from a NextSeq run, and the quality plot looks really strange, and I am loosing a lot of the data (around 75%) when running DADA2, mostly at the chimera removal step. I did a little pilot run on MiSeq, and the data turned out good, but our sequencing center just got the NextSeq, so I thought I would use it for the full run but the data from the run seems to be poor.
For background, i am running some short amplicons for detection of mammals from eDNA samples. I removed all of the non-biological sequences with Cutadapt prior to running DADA2. The amplicons are around 110 bp.
The quality plot looks like this,
Which is like nothing I have seen before. Why are there not Whisker plots at most positions?
For reference, this is what the plot looked like for the pilot MiSeq run:
Any thoughts would be helpful.