How to assign the reads to two very similar gene sequences

[Xi Chen]

Hey people,

I have a question about the alignment. When I analyze the RNAseq data from mouse, I found there is a huge difference on specific Gene-a between WT and KO. Actually Gene-a is a pseudo gene and has a parent functional gene as Gene-A. I checked the sequences between Gene-a and Gene-A. To my surprise, they are almost the same only except for 3' UTR region. So I want to ask why the reads assigned to Gene-a not its parent Gene-A? (Gene-a is on chromosome X and Gene-A is on chromosome 15)
Thanks!