Can QIIME 2 read Nucleotides?

If I have a primer that has nucleotides like the one below can QIIME 2 read the nucleotides or do I have to give all the combinations of that nucleotide?

Primer with nucleotides:
GTGY CAGCM GCCGCGGTAA

All the combos it could be: Y(c or t) and M (a or c)
GTGcCAGCaGCCGCGGTAA

GTGcCAGCcGCCGCGGTAA

GTGtCAGCaGCCGCGGTAA

GTGtCAGCcGCCGCGGTAA

If I do have to indicate all the combos what is the best way to do that in QIIME2?

Hi @jgcx - I'm not sure we can answer this question without knowing what command or commands you're interested in - can you please provide us with additional context? Plugins like q2-cutadapt are definitely able to interpret IUPAC wildcards, but others don't need to, so it really just depends. Thanks!

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@thermokarst Hello, can you please explain what you mean by wildcards? Do you mean that all of your commands if given a primer sequence can distinguish between a nucleotide and base pair? I would like to know if all the commands that utilize primer sequence information can recognize a nucleotide (Y, M, P, etc) vs a base pair (A, T, G, C) since the nucleotide code for different base pairs, Y(c or t) and M (a or c)?

Sure!

It depends! Please see my previous answer. As well, I encourage you to read up on the ethos and design of QIIME 2:

https://docs.qiime2.org/2021.8/tutorials/overview/

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