I am analyzing Miseq sequencing data and found good quality Forward and Reverse data. I did some tests with different truncation values and I'm unsure if I should provide the value 150 for the --p-trunc-len-f and --p-trunc-len-r parameters or if can I directly provide the value 0. In the latter case, by providing the value 0, could it have erroneous taxonomy results, considering that no sequence smaller than the given value will be discarded?
Testing the command below I obtained non-chimeric results between 55% and 84% (which doesn't seem bad to me), but when providing the value 0 in --p-trunc-len the results are even better: 75 to 90% . Which option would return more reliable results?
qiime dada2 denoise-paired
Thank you very much for the help!