-fr and -rf flags for strand specific RNA-seq

[asethi-1]

Hello,

I am mapping some paired-end strand-specific RNA-seq. This data maps logically with STAR, with the majority of reads in sense with their transcript. However, this is not the case in Magic-BLAST. Where can I find documentation on "-rf" and "-fr" flags for magic blast? How can they be used to achieve strand-specific mapping?