I’ve done ITS2 sequencing (MiSeq 2x300 bp V3 ) and my target size should be around 400-500 bp. I’m having a hard time deciding the parameters for DADA2 denonising and specially trunc-len parameter. The problem is that my data quality does not look so good and I’m not sure how to handle this kind of data.
DADA2 will take care of the data by correcting possible errors but I’m concerned about the data quality dropping at the ends of the reads. In bacterial data 16s for example it is okay to use trunc-len to discard reads that start to be bad quality reads. But in ITS it is not recommended to use that because of the natural variability.
What parameters should I use to be sure that the bad quality reads are discarded. Or is this data quality so poor that I should not use this data-set?
Thank you for advance!