Hi everyone! I have a few questions about about ITS processing within qiime that I’m hoping someone would be able to answer. I have read through the ITSxpress and cutadapt method tutorials posted here and wanted to make sure I was doing everything correctly as I am having a lot of unidentified taxonomic sequences (anywhere from 33-98%).
- Is there a difference to using ITSxpress vs cutadapt? Should I use one over the other or both sequentially?
- When using cutadapt do I use the adapter and primer sequence of both my forward and reverse primers? The cutadapt ITS tutorial mentions using the reverse complement - do I need to do that also and if so how if I have 2 different adapters/primers.
I’m sure I’ll think of more questions but I figured I’d start with the basic stuff.