I am planing to find out differential gene expression between two samples (infected and non infected RNA-seq data of avian species from 454 GSFLX+ PLATFORM), but there is no reference genome available. So I am planning to perform a De No transcriptome assembly with Newbler. How can I determine the number reads assembled to particular gene (I have only contigs from the assembly) for statistical significance testing. Are any normalization procedures required? Please suggest some common software for this analysis.