Basically you have the assembled transcriptome from RNA-Seq data. May be first you need to annotate the transcriptome using some pipeline like trinotate. See few posts below:

• Annotating sequences after de-novo Trinity assembly and RSEM analysis...there must be an easier way!
• Annotating A Novel Transcriptome Assembly

Once you have annotated the transcritptome, you can think of different ways to identify novel contigs with coding potential.

P.S I have never done this sort of analysis, so its just my idea.

What kind of organism are you working on?

CLCBIO should have an in-software annotation mode. You now should annotate the assembly. You should also check the assembly statistics to see if it is deemed a good assembly. Additionally Have you completed QC on your reads? In order to obtain a good assembly you should remove low quality bases and short sequences.

You can use Oases and followed by cap3 to get unigene form your contigs sequence. After that you can annotate unigenes by using various tool like blast or KEGG.