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!
@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)?