expression evidence for overlapping genes

Question

[GR]

Hi All,

Can anyone point out to me method/tool to get the expression evidence for overlapping genes.

Thanks, Rit

[ATpoint]

I guess any quantification tool that handles stranded RNA-seq library prep. Without stranded prep, it might be difficult. I recommend salmon.

[GR]

correct me if I am asking a dumb question. How does stranded RNA-seq solves my problem. Overlapping gene can exist in different frame, not necessarily from different strand.

[ATpoint]

True. Still salmon has an elaborate way dealing with multimappers which would be the case here.