Identifying ago2 enriched genes under 2 different conditions
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.
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The authors of Tophat suggest not to use it, but Instead use Kallisto. Nice tutorials.