I have a dataset with multiple markers (4) that were combined prior to indexing.
I would like to use cutadapt to a) trim primers, and b) separate reads from each marker.
I have done this before in the standalone cutadapt, but is it now possible to do it within QIIME2? I know that it was not last time I checked, but was wondering if it is now possible in the new version.
I have been trying to interpret open issues #10 and #29 as they seemed relevant, but with my limited knowledge I was not able to fully understand the outcome.
Basically, what I would like to do is trim primer set #1, and have the untrimmed reads outputted to their own artifact. Then I would run cutadapt again for primer set #2 on that “untrimmed" artifact, and then repeat for primer sets 3 and 4, until I have 4 separate artifacts with primers trimmed for each marker.
Does this make sense, and is it now possible in QIIME2?