cuffmerge assembly vs denovo assembly of RNAseq data

[skm]

Hi all,

I have RNAseq data of stress-control of various tissue of a plant. I am doing differential gene expression. In addition, cuffmerge provides me with transcripts assembled. But is this a valid transcriptome at publication ? Or should I go for a denovo assembly of the RNAseq data ? and for a comprehensive assembly of all the tissues together ?

I have not come across publications reporting cuffmerge transcriptome.

please advise.

Thanks

regards
skm