I've downloaded RNA-seq data (Hs) from a published paper and to my surprise the control condition is PE and the 2 conditions are SE. No replicates.
They've used this data to determine differential exon usage between control vs condition 1 and control vs condition 2 using a "home-brewed" analysis after mapping. To answer the particular biological problem I am interested in, cufflinks (and cuffdiff) is ideal because it should allow me to extract exactly the information I am interested.
The question is: is it even possible to use cufflinks (+cuffdiff) to analyse control (PE) vs condition (SE)?