Trim based on quality score not the sequence position

[Nicholas_Bokulich]

@Negin

the way trimming works with qiime 2 is that we should trim based on the sample position where the quality drops.

That is a misunderstanding.

1. QIIME 2 has multiple different approaches to trimming available.
2. For manual trimming we usually recommend trimming where quality drops off below a threshold (my rule of thumb is where median Q drops < 20), not just arbitrarily wherever quality begins dropping.

One reason why we usually recommend manual trimming at a specific site is because otherwise identical sequences trimmed to different lengths will be considered different ASVs/OTUs, skewing diversity estimates. This is less of a concern with paired-end sequences, as sequences are being merged back into complete amplicons or dropped if they are too short.

@Negin

I usually trimmed my sequences based on the primer sequence and the quality score below 20 using trimmoatic.

You can do that in QIIME 2 as well! See the quality-filter plugin. Additionally, dada2 has a --p-trunc-q parameter to perform this type of trimming (e.g., see here).

@Negin

for trimming the primer, should I use --p-trim-left 19 if my primer is 19 nucleotide?

Yes, if your primers are still in the sequence (they aren't always, depending on the sequencing protocol you used).

I hope that helps!