For cutadapt option

User Support
2

Hi @yogurt,

  1. If your sequencing protocol does not make use of primers with frameshifting nucleotides, e.g. Lundberg et al. 2013, then you can simply use the trim and truncation options to remove the primers. I personally, like to use cutadapt (with the --p-discard-untrimmed and --p-match-adapter-wild-cards) regardless of how the sequencing was performed, as it serves as a form of quality control. That is, if you can not detect the primers in the sequences, chances are that the rest of the read is not very good, or is spurious. So, you discard them.

  2. See this:

-Cheers!
-Mike