When trimming primers, does the “qiime cutadapt trim-paired” function interpret degenerate bases?
qiime cutadapt trim-paired
If so, what should my “–p-error-rate” be to account for that?
Based on this issue, I think cutadapt does support degenerate bases so your command should work.
I’m not sure… I think your best answer is going to come directly from the Algorithm details page or the cutadapt docs.
Hi @Tyler_Carrier, the
–p-error-rate should only count towards mismatches.
To clarify, cutadapt makes use of IUPAC codes by default, i.e.
--p-match-adapter-wildcards. Thus, if a base in the sequence matches given the IUPAC letter of your primer / adapter, then it should not count as en error / mismatch.
For example, if your primer contains an
M then the bases
C will be considered a match at the corresponding position of your read. Other bases, will be considered a mismatch. Assuming the sequence is the same strand as your primer sequence in this case.
Note, you can also enable the
--p-match-read-wildcards to make use of any potential IUPAC bases in your sequences.
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