Align_Estimate_Abundance pipeline using merged assemblies of Trinity and Other tools possible?

[ErwinST]

Hello,

Has anyone tried or have idea if it is possible for Trinity /align_and_estimate_abundance.pl to recognize a transcript fasta that is made from a merged assembly

of Trinity and Soap-denoTrans.. I have not done yet but I am looking to merge the transcript assemblies using EvidentialGene tr2aacds pipeline.

I am guessing the issue could arise from the contig naming...(?)

It is with our great interest to merge assemblies from the two tools, and I would like to exploit the simplicity of Trinity transcript quantification pipeline (for Salmon, Kallisto and RSEM). Any idea tweaking needs to be done? Or if I'm better off just using RSEM, salmon etc standalones  after merging (but tbh is a path I don;t wanna take, if possible). 

Thanks,