RNA-seq: Comparing 2 strains (same experimental conditions)

Question

[Cricket]

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.

[Fabio Marroni]

1. I think so, but makes sense only for genes that are shared and have the same function in the two strains
2. Yes, you just use the different strains as you would use two different conditions. It is advisable that you have at least three replicates for each strain and each condition.

[Cricket]

Thank you @Fabio. I am currently getting Tophat2 errors, but I will post the problem in a new question (https://www.biostars.org/p/197689/).