Greetings.

I have data that was used for RNA-seq analysis. The experiment involved two E. coli strains in two different environmental/experimental conditions. I compared the differences in gene expression for each E. coli strain between the two different experimental conditions using Tophat/Cufflinks.

I was speaking to a colleague recently, and he was interested in seeing the difference in expression for the same experimental condition between the two different strains -- again using Tophat/Cufflinks.

I understand why he would like this information, but it does feel a bit like comparing apples to peaches.

1. Is this approach legitimate?
2. Is it possible to do this with Tophat/Cufflinks?
3. Does anybody know of a better approach for comparing gene expression between two strains?

Thank you in advance.