RNA-seq data analysis

[Rachel]

Hi. I am working on the Illumina RNA-seq data for an eukaryote. The reference sequence i am using is not complete (alot of contigs). I had assemble the RNA-seq reads into contigs using the de novo approached. However can i know if there is any bioinformatic tools that i can used to assemble the mRNA into a scaffold? or what else can i do to compare the expression level? My have uninfected with infected data.

thanks