I am wanting to separate pooled PCR products (paired-end) by their differing primer sequences, which have been demultiplexed.
I initially tried cutadapt, which was great until I realized that the output file was containing all the sequences - trimmed and untrimmed. So, I have tried various ways to remove the unwanted sequences to no avail using Qiime 2 - yet.
My code at the moment:
qiime cutadapt trim-paired
The error I am getting is:
Error: no such option: --p-discard-untrimmed
*same message if I change it to --o
I feel like I am missing something, as this is a filtering option. I previously did this step in Qiime 1, but would like the entire pipeline to now be in Qiime 2. Is this possible?