I perform the cutadapt cuts by generations when talking about paired end cuts. I mean first I cut the adapters with code like:

cutadapt -j 45 --pair-filter=any -a AF1=AGATCGGAA -A AR1=AGATCGGAA --rc SRR9201174_1.fastq SRR9201174_2.fastq -o ./cortadas/S1_174_1.fastq -p ./cortadas/S1_174_2.fastq

then I perform a second generation cut because I find with paired end reads cutadapt is not as good:

cutadapt -j 10 --pair-filter=any --trim-n --poly-a --max-n 0.1 -q 20,20 -m 100 -u 11 -U 11 ./cortadas/S1_174_1.fastq ./cortadas/S1_174_2.fastq -o ./cortadas/S2_174_1.fastq -p ./cortadas/S2_174_2.fastq

I dont know if to trim reads like that on librarys is already obsolet