Comparing the RNAseq analysis data

Question

[prp291]

I am analyzing RNAseq data using CLC genome workbench. I am using the both available unigene build (because whole genome is not available) genome and assembled genome as a reference. I am always getting the less number of count fragment for my assembled genome in compare to unigene build. But number of contigs in assembled genome is high than unigene build. Can anyone suggest to improve my experiment?

[Biomonika (Noolean)]

Could you provide more information, possibly including numbers you are getting? I am not sure if I understand what you are asking.