Differential expression for 454 single end and illumna pair end reads

[rnathg]

Dear all,

I have four samples i.e two from 454 (single end) and two from illumna(pair end). I mapped all these samples to non redundant reference set of sequences which contains assembled(denovo assembly) unigenes from all the four samples. My questions are

1) How do i count number of reads mapped for single end and pair end libraries as there will be more number of counts in pairend libraries compared to single end?
2)Do i need to normalize the counts for doing differential expression between these samples? if so how i normalize them in order to see the differential expression?

Hope im clear with my questions. Any more information im happy to provide i think im stuck . please help me.

Thanks in advance,
Ranga