Hi, thank you for your respones! I have a few more questions I wanted to clarify with you.
--p-trunc-len: Position at which read sequences (forward or reverse) should be truncated due to decrease in quality. This truncates the 3’ end of the of the input sequences (i.e. the right side) , which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded.
Wouldn't the --p-trunc-len discard all the sequences greater than this value since this command would be truncating the right side? So if I set the value to 150, wouldn't that get rid of all the bases above the 150 position, and not below?
In addition, what happens if I set the value of --p-trunc-len to higher than the whole sequence length? For example, if my whole sequence is around 150 bases, but I don't know the exact length, so what if I set the value to 151? Would it not truncate anything if my base was shorter than 151?
Thank you again!