Why does the Pair-End RNA library exhibit a significant disparity between the mapping results of R2 compared to R1?

Question

[Carolina]

We conducted total mRNA RNA-seq using Illumina technology and encountered significant disparity in the mapping between R2 and R1. We are considering potential issues with trimming; we utilized FastQC and Fastp. We are exploring other possibilities

[rpolicastro]

You should provide the code you ran otherwise it will be difficult to help.

[GenoMax]

Do not align paired-end data independently, if that is what you doing.