Identifying ago2 enriched genes under 2 different conditions

Question

[ancient_learner]

We wanted to see the effect of particular gene expression (gene A) over mirna targetome. for that we have designed our experimental setup as follows

total cell RNA lysate(TL)          RIP                 Results
Condition1 ( geneA-/- cells)  condition1      Ago2 enriched genes in cond1 
condition2 (geneA ER cells)   condition2      Ago2 enriched genes in cond2

We followed Tophat-htseq-DESeq2 procedure to get Ago2 enriched genes in each condition by keeping TL as control and RIP as experimental for each condition. so far its good. but now we want to obtain the genes which are highly enriched by ago2 in condition2 over condition1 with good statistical significance. what is the prescribed procedure for this? Any help will be appreciated.

[Chirag Nepal]

The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials.