Remove Primer in paired-end demultiplexed file

Technical Support
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Hi @mohsen_ej,

Thank you for attaching the QZVs. You'll want to add the following flags, which were also mentioned in the posts I linked above:

--p-match-adapter-wildcards --p-match-read-wildcards --p-discard-untrimmed

You'll likely not need --p-match-read-wildcards, but it does not hurt to throw it in. :baseball:

This will allow cutadapt to match the IUPAC codes in your primers (i.e. W, V N,...) with the reads, and discard any sequences in which it could not find both primers. The latter ensures you only have sequences that were trimmed.

So your full command should be:

qiime cutadapt trim-paired
    --demultiplexed-sequences paired-end-demux.qza \
    --p-front-f CCTACGGGNGGCWGCAG \
    --p-front-r GACTACHVGGGTATCTAATCC \
    --p-match-adapter-wildcards \
    --p-match-read-wildcards \
    --p-discard-untrimmed \
    --o-trimmed-sequences paired-end-demux-trimmed.qza

-Cheers!
-Mike

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