I am quite new to qiime2 but I am eager to learn how to use it. I am having trouble to decide were to truncate the sequence in DADA2.
I got my demultiplexed paired end sequences and the length of my forward primer (ITS9) is 23 bp and of reverse primer (ITS4) is 20. The amplicon lenght of should be between 240-460bp. I have also uploaded the interactive plot visualization. The sequence quality of the forward reads looks good but the quality of the reverse reads is lower and I don’t know where to truncate. It would be great if you all can help me in understanding and deciding where to truncate my sequences.
Here my command in QIIME2
qiime dada2 denoise-paired
Thank you in advance,