I am using STAR to map reads from paired-end mRNA sequencing.
I mapping stat look fine overall, but I had in all my samples about 15% "unmapped: too short:.
When looking into the unmapped reads, I discovered there are reads that do not map when I map them as paired-end. However, when I map R1 and R2 separately, they do map fine.
I just do not get why the pair then would not map, they have a full and perfect alignment and also the quality score for the bases is good.