Cutting ITS primer sequence produces error because of IUPAC code limitations

[SoilRotifer (Mike Robeson)]

Hi @esther

Cutadapt can handle IUPAC, but note that I is not a standard IUPAC label. See my post here that describes what I is and how to handle it:

Handling ambiguous nucleotides in database construction

Hi @devonorourke & @Nicholas_Bokulich, I have had similar issues with I characters when using vsearch and other similar tools. Keep in mind that I stands for the chemical Inosine / deoxyInosine, which you can order as part of your oligos (e.g. from IDT). That is, it functions literally as an ambiguous N base. So, wherever you find and I replace with N. For example, take a look at the CO1 blocking primer we made in our swine diet paper. As for the U --> T bit… In the past, when I put that set o…

-Best wishes!
-Mike