Is the truncating parameter necessary to use? I have different result with different integer with truncating parameter!
Should I use it? is it necessary? It just remove NTs from 3 prime side so what is the use of this?
The parameter is not ‘necessary’ to use per se but is strongly recommended. Your analysis will suffer drastically if you include low quality reads in your run. There are countless threads on this forum discussing how to select these trim/truncate parameters and most of them include an explanation of what the benefit of these are. I suggest start by reading through some of these.