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expression evidence for overlapping genes

Hi All,

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

Thanks, Rit

rna-seq
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written by GR GR

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

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written by ATpoint ATpoint

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.

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written by GR GR

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

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written by ATpoint ATpoint

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