I have a set of demultiplexed fungal ITS1 reads, and I'd like to run a multiple sequence alignment with these R1 and R2 reads using MUSCLE.
I've used MUSCLE with metagenomic shotgun data, not amplicon data, so I am not sure about how to preprocess my sequences before the MSA.
Should I merge my R1 + R2 reads, trim them, then run them through a MSA? Or can I run R1s and R2s in through their respective MSAs (as raw reads) and see what my results are?
I would love your feedback, thank you!!