I have noticed a strange behaviour when using Rsubread in a recent bacterial RNASeq dataset. The use of the nTrim parameters lead to a change in the order of the reads provoking that they do not pair properly (check below). I have tested the same parameters using other samples from a different library and different bacteria and I have not been able to reproduce this issue. I also run this same samples on Star using the parameter clip5pNbases and it worked fine.
Does anyone have an idea about why might this be happening?