Thank you very much for your script. I read this script and I have a few questions.
1> Is this script will remove the primers (provided) and any preceding sequenses (including barcodes in that case)? If so, --p-front-f and --p-front-r parameters will do this work. Am I correct?
2> I also notice that there are other parameters such as --p-adapter-f and --p-adapter-r.
What is the difference between --p-front-f and --p-adapter-f ? I read the manual. It seems --p-adapter-f and --p-adapter-r are for the reads with adapters/barcodes on both forward and reverse reads. Should I also provide my reverse compliment primer sequences by using --p-adapter-f and --p-adapter-r, just in case (as I don't know how the sequencing arrange the adaptors)?
If I do need to add these parameters, --p-adapter-f should be reverse complement sequence of my REVERSE primer and --p-adapter-r should be reverse complement sequence of my FORWARD primer?
Or --p-adapter-f should be reverse complement sequence of my FORWARD primer and --p-adapter-r should be reverse complement sequence of my REVERSE primer.
3>After I run remove barcodes and sequences using cutadapt. I need to run DADA2. Usually, it will still have low quality score bases at the beginning or end of the sequences. I need to cut off these. Normally, what Q-score do you choose? 30, 35 or 40?