Using generated transcriptome assembly by two assemblers

Question

[seta]

Dear all,

I performed de novo transcriptome assembly for a non-model plant using two assemblers, CLC genomic workbench and Trinity tool. Both assembly sounds good, I would like to use generated information by two assemblers, is there any idea to this end? merging both assemblies and redundancy reduction may be one possible answer, but I'm not looking for merging. Your feedback would be highly welcomed.