I am follwing the PacBio CCS Amplicon SOP v1 for Qimme2 and I can't seem to get cut adapt to work. The command runs but the output files are empty, the naming + location is correct.
I've also been sent this message from the sequencing facility but I do not understand how to incorporate this into my code: "There are not adapters in the data. The data only has primer sequences. The adapters are removed during demultiplexing. I would suggest not using cutadapt for primer trimming as well. Within your cutadapt you are using –p-adapter twice whereas the data is single ended. If you want to continue using cutadapt, I suggest putting … between forward and reverse primer – like --p-adapter AGRGTTTGATCMTGGCTCAG…TACGGYTACCTTGTTACGACTT. That way cutadapt knows it must look for both the primers in the same single ended sequence. Within qiime dada2 denoise-ccs there is an option to specify –p-front parameter (forward primer) and –p-adapter (reverse primer). You can directly use that to remove primers and denoise the data."
Thank you for bringing this question to the forums!
First, I want to clarify that the SOP is from the LangilleLab Langille Lab · GitHub
I can still help out with the Qiime2 part and offer some general advice.
I concur with the advice from the sequencing core:
You can skip this step!
You can also do basic read trimming with DADA2, as mentioned here: