prodigal on metatranscriptome assembly

[ckeuschn]

Hi,

I have assembled a metatranscriptome and wonder now if gene calling for downstream analysis is necessary or not. The contigs should be ORFs anyways as they are transcribed right? However, when I do run prodigal on the contigs I get slighly lower number of ORFs than the contig number. Does that makes sense to you?
Many thanks for any thought and advice!