Dear all,

I have a question regarding the analysis of our RNA seq data:

First let me layout the data we have:

We 2 groups X and Y, in each group we measured RNA seq on 3 individuals, for each of these 3 individuals we have read counts (reference, alternative)

At a SNP we want to get a p-value that expresses how the ASE is different from group X to Y

So in the following (made up example)

      Ref   Alt

X1 100   30

X2 50     20

X3 500 160

Y1 50     50

Y2 40     40

Y3 70     70

From the data we can clearly see that in group X the ratio is around 3:1 for ref:alt, while in group Y the ratio is 1:1

Which test do I need to use?

I looked into Chi Square testing which seems to be able to give me a pvalue per sample, but how do I then compare group X versus group Y

When looking for more info I came across the Cochran-Mantel-Haenszel chi-squared test, which also doesnt seem to fit the data, since the individual X1 is not the individual Y1 under a different condition it is a completely different individual, so I cannot add individual as a stratum variable.

Any suggestions ?