Assemble 3'mRNAseq with standard RNAseq

Question

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Hello,

Is there a protocol or something like to safely assemble 3'mRNA-seq data with standard RNAseq data, onto a non model organism, in order to merge separate assemblies into a single consensus annotation? They got a very similar experimental design, as the standard RNAseq is a reproposition of the first, although the first is a single-end and the latter is a PE experiment.

Cheers