some questions about cutadapt demux-paired

[SoilRotifer (Mike Robeson)]

What primer set and amplicon region are you using? Also, I often recommend that users apply the following flags when using cutadapt:

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

For more detail see:

The results of dada2 after cutadapt showed that there were still primers

Hi @LiyingXie, I would like to add that since your primers contain IUPAC ambiguity bases, e.g. H, V, W. I would highly recommend that you add the following flags: --p-match-adapter-wildcards, and --p-discard-untrimmed. That is if the former flag is not enabled, only ATGC matches will be allowed, any ambiguous bases will count as a mismatch resulting in cutadapt in not “finding” the primer sequences, thus not removing it. The latter flag, will discard any sequences in which you can not find the …

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 ensu…

-Mike