I am trying to remove primers using cutadapt in qiime2. I have demultiplexed paired-end data. I first ran my data through dada2 without any trimming, and the resulting seqs contain both the F and R primer, with some additional bases on either end. In the trim-paired documentation, it says to use the --p-adapter for linked primers, and follow details from cutadapt.readthedocs.io.
Thus I ran the following code:
qiime cutadapt trim-paired
–i-demultiplexed-sequences demux.qza
–p-adapter-f ACTGGGATTAGATACCCC…CTAGAGGAGCCTGTTCTA
–p-adapter-r TAGAACAGGCTCCTCTAG…GGGGTATCTAATCCCAGT
–o-trimmed-sequences demux-trimmed.qza
–output-dir output
–verbose
But I got an error saying:
cutadapt: error: Character ‘…’ in adapter sequence ‘ACTGGGATTAGATACCCC…CTAGAGGAGCCTGTTCTA’ is not a valid IUPAC code. Use only characters XACGTURYSWKMBDHVN.
Clearly it is not recognizing the “…” between the primer sequences. This is puzzling because I found this past forum entry that said that such syntax worked well (but appears to have been for single-end data).
Do you have any suggestions for getting this to run correctly. I am relatively novice at this, so it is likely that I am missing something simple.
