Cuffdiff between samples with different technologies

[DAnand]

Hi All,

I have two-mouse RNA-seq samples, one is single-end and another is paired-end from illumina platform.

Sample 1- Single-end reads X 3 replicates
Sample 2 - Paired-end reads X 3 replicates

I have performed 'Tophat' and 'Cufflink' for these samples separately. I want to know whether it is appropriate or possible to perform 'Cuffdiff' between samples from different technologies to identify differentially expressed genes? If not, is there any other way I can find out DRGs between sample 1 and 2?

Please suggest.

AD

[bastianwur]

Are they supposed to be the same biologically?

What we do: Cross-assemble them all together, map the reads back, perform PCA on the (normalized) counts.
Should tell you if the sequencing technology makes the biggest difference.