I have been using Qiime2 to generate ASVs of V3-V4 sequences by trimming off the primer sequences and then denoising with DADA2. I am using qiime2 2020.6
I noticed in my ASV sequence output I often have ASVs that are identical over the entire V3-V4 region however are a different length where one will have a primer sequence still stuck on the end of it that didn’t get trimmed off because of a SNP or small INDEL in sequence corresponding to the primer.
I tried to use cutadapt to remove read pairs that don’t get trimmed but it didn’t resolve the issue:
qiime cutadapt trim-paired
Has anyone else seen this issue? My assumption is that -p-discard-untrimmed is keeping pairs where only one end was trimmed, but if that is the case then is there a workaround to remove these bad ASVs?
Thank you all for any help!