Cutadapt for linker and primer

[SoilRotifer (Mike Robeson)]

Hi @Man,

The issue is that you are feeding the entire construct into cutadapt, when you should only be providing the PCR primer sequences. Here is a related forum post that should help:

Remove Primer in paired-end demultiplexed file

Hi @mohsen_ej, if you search the forum, you’ll come across many examples of how to use cutadapt. There are quite a variety of ways to leverage this tool. You’ll likely just want to specify your specific primer sequences not the entire construct. That is, your primers are likely these (anything after the …GAGACAG): --p-front-f CCTACGGGNGGCWGCAG \ --p-front-r GACTACHVGGGTATCTAATCC \ Here are a couple to get you started: -Mike