Cutadapt paired end read through

[Nicholas_Bokulich]

Hi @SarahH,
The options you are looking for are --p-adapter-f and --p-adapter-r. We have a tutorial demonstrating how to use this, using the example of fungal ITS where read-through is a common issue (looks like that's what you are working with too!):

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QI…