Trimming the first 5 low(er) quality bases from forward and reverse reads results in 25% more sequences removed as chimeras

[Nicholas_Bokulich]

Hi @ngarcia,
Are primers trimmed from these reads? This can often lead to unexpected chimera filtering, e.g., see this topic:

Low sequence retain after DADA2 step

Hi! i know this has been asked lots of times, but i'm getting very low sequences after DADA2. This seqs correspond to V3-V4 region (expected amplicon size ~460) I tried triming F- 280 and R- 220 and without trim, but i lost A LOT in both, any advice? or help? fulldenoising-stats.qzv (1.2 MB) Denoising stats for NO trimmed. shortdenoising-stats.qzv (1.2 MB) Denoising stats for trimmed palmsequences.qzv (290.7 KB) sequences it self.

You could also try adjusting the min-fold-parent-over-abundance parameter, there has been some interesting discussion on the forum regarding how and when to adjust this parameter, could be worth taking a look: Search results for 'min-fold-parent-over-abundance' - QIIME 2 Forum

Good luck!