Dear edgeR users and developers, we used Solexa sequencing in order to detect RNase E processing sites. Therefor we splitted a RNA sample and treated one half with RNase E prior to cDNA synthesis and sequencing. The libraries differ in size (1.918.953 and 1.208.586 reads respectively) which clearly necessitates a normalization step. Furthermore we expect site specific differences rather than differences in the accumulation of the full length RNAs. So I want to ask, if it is appropiate to do a single nucleotide based normalization with edgeR and do you think a reliable basic normalization is possible without replicates? Thank you for your comments. Best regards Jens