Missing taxa using Unite classifier for ITS2

[SoilRotifer (Mike Robeson)]

@umanand

When I took both F and R sequences for 16S, the percentage of merged non-chimeric sequences were only 36%

Are you losing data at the merge or the chimera filtering. If merging than I suggest playing around with the truncation parameters, and/or try deblur for denoising. If you are losing many reads due to chimera checking I'd suggest setting DADA2's parameter --p-min-fold-parent-over-abundance 8 as per:

Trimming output problem

Thanks for sharing these @Liviacmg. I think for those samples, in which you're losing more sequences, appears to be due to losing proportionally more due quality filtering rather than chimera removal. The drop from denoised to non-chimeric isn't as much of a drop as the quality filtering. This could probably be helped by truncating a little more. Another option is to adjust the --p-min-fold-parent-over-abundance to 8 or 16. I wouldn't suggest any higher than that. This is based on the followin…