how to do test on RNA-seq data like this

[shuixiangyuer]

Hi, all

I have two groups of RNA-seq data (A and B), with both two biological replicates within groups(A1, A2 and B1, B2). For each replicate, the reads are mapped two genomes(X,Y). Now i have counted the mapped reads for each orthologs between X and Y. Next, i want to do statistic test on expression ratio of X/Y between groups. I don't know which model or method could be used, anyone who can give suggestions. Thanks.

[DonDolowy]

I am in a similar position and what I have chosen to do, is to run the Tophat - Cufflinks - Cuffdiff - cummeRbund pipeline. In addition, I am running Tophat - HTseq - DESeq.

In the end, my idea is to end up with two lists of DE genes and then intersect them. Those genes captured by both techniques must for sure be DE.