DADA2 : low non chimeric read counts after denoising step , --p-min-fold-parent-over-abundance

HI @Sue, the suggested values are outlined in this post, along with references. I'd suggest not going above 16 if possible.

To help I'd also lower the truncation values too... by default DADA2 requires at least 12 bp of overlap. I'd suggest reading this post for more detail.

1 Like