I’m new to qiime2 and I am currently trying to quality check my sequences. Many guides suggest using dada2 but I am hesitant to truncate my data as it doesn’t appear that the ends are drastically different in quality to the rest. Would you suggest I truncate or not truncate? If so, from what bps would you suggest?
What primers did you use for this data, and what length is the expected region?
The truncation length is not just about removing low quality sequences, it is also about choosing an optimal overlap length for merging the paired end reads.