Cutadapt doesn't recognize all adapter sequences

[llenzi (Luca)]

Hi @elephas,

Welcome on the forum!
If you have not fixed the issue yet, I would suggest you to trim the PCR primers instead of the sequencing adapters, which should
be following the adapter sequences in your reads (although it may depend on the library prep used).

Also, I suggest you to look at the following thread:

Remove Primer in paired-end demultiplexed file

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. 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 en…

and add '--p-match-adapter-wildcads' and '--p-discard-untrimmed' as options!

Hope it helps