Degenerate bases

Hi all,

When trimming primers, does the “qiime cutadapt trim-paired” function interpret degenerate bases?

For example,

qiime cutadapt trim-paired
–i-demultiplexed-sequences import.qza
–p-error-rate 0
–o-trimmed-sequences import_trim.qza

If so, what should my “–p-error-rate” be to account for that?


Hello Tayler,

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.


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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 A or 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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