Off topic:Differential Expression From The Single End Read

Question

[Senthilkumar]

Possible Duplicate:
Measuring differential expression using RNA-seq in organisms without a genome or transcriptome?"

I have NGS of single end read for non-model organism (control and experiemnt) done by commereical CLC bio. could anyone help me my quires. How differential expression analysis will be made. Sincee the contig of control library not match with the same contig of experimeent. any procedure or related publication for the same.