Denovo RNA seq

Question

[kanwarjag]

I am trying to find which tool or work flow is best/ commonly used for de novo assembly of RNAseq PE data? I want to do two things,. 1. map it back to reference genome and calculate transcript level expression between treatment vs control 2. The unannotated transcripts will be separately accessed and will be corelated from protein expression of same cells. Any suggestion.

[ATpoint]

stringtie

[kanwarjag]

So If I understand correctly String tie can work with reference as well as without reference -de novo. Just one clarification Do we use Trinity for assembling de novo and then use String tie?