I am recently work on a small project that need to determine whether 2 genes are linked each other. We have A, B genes, they are very close in the mouse genome.

Bascailly, we inserted loxP sites into the locus of a specifc exon of gene A in mouse genome, the mouse backbone already carried aonther floxed gene B. Then, we cross this AB double flox mice with Cre mice to knowck out the two genes at the same time.

There are two possiblies about the double deletions.

1. large deletion from gene A to gene B
2. gene A deletion + gene B deletion (separately)

Is there any way to detemine what will happen by using RNA-seq data?