Is my DADA2 outputs nomarl?

[crusher083 (Valentyn Bezshapkin)]

Hi,

You might want to take a look on that thread:

DADA2: loss too many reads after filtering

Hi Qiime2 fellas, I'm working with similar data (DNA extracted with PowerSoil, same primer pair, plus a organellar blocking primer set, Miseq sequencing), I also lost a lot of data during dada2 step (see image below) even after trying all variations of metaparameters (FYI, I truncated fwd at 290 and rev 260, trimmed first 10 bp, this last one helped a lot), [image] I might sound mean, but with the combination of protocols we used, apparently we get low throughput, I even got a sample which o…

The quality of the reverse read is OK. There are a lot of variables that influence it.

To get results try changing --p-min-overlap parameter.

Cheers
Valentyn