can i skip cutadapt??

[svbreqwaiu01 (Seoki)]

recently i receive rowdata from NGS center..
and i start analysis using QIIME2

i want 'cutadapt', so i ask primer sequence to NGS center..
but center reply to me "it is secret"

if it is neccessery, i request to NGS center....

thank u for reading

[SoilRotifer (Mike Robeson)]

Hi @svbreqwaiu01,

You do not need to use cutadapt. You can simply use the deblur / DADA2 trimming options to snip off the first 20-30 bases of both the forward and reverse reads. The NGS center should at least be able to tell you how long the forward and reverse primers are, so that you can trim / remove them.

Here is a study, that I was involved with, in which proprietary primers were used. Fortunately, the company was willing to let me know how long each of the primers were (forward was 16 bases, and reverse was 24 bases), and I added this information to the MIMARKS compliant metadata in my GenBank SRA submission. This way, others can process the data properly.