Hi @ek_97, welcome back!
That's a great question! I'll go over what each of these parameters does below, which should provide some clarification on your question above.
--p-trim-left: Position at which read sequences (forward or reverse) should be trimmed due to low quality. This trims the 5’ end of the input sequences (i.e. the left side), which will be the bases that were sequenced in the first cycles.
--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. After this parameter is applied there must still be at least a 12 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed.
If you set
--p-trim-left to 0, no reads will be trimmed from the left side of your sequences. However, if you set
--p-trunc-len to 0, you will truncate all reads from your sequences (since this is truncating everything greater than the position specified - which in this case would be 0).
If you'd like to use the full length of your sequences, I'd recommend just leaving out these parameters altogether - your sequences will not be trimmed/truncated unless specified by the above parameters.
Hope this helps!