expression of adjacent genes are affected ?

[szy0931]

I am doing RNA-Seq to a mutant strain of Salmonella.
One gene is deleted.
By RNA-Seq, expression of two genes next to the deleted gene is reduced compared with wild type.
The two genes are in one direction and the deleted gene is in the opposite direction.
Based on current knowledge and deletion construction, expression of the two genes should not be affected.

So, do you think if reduced expression of the genes are REAL or it could be caused by mapping because they are located next to the deleted gene

Thank you very much!

[dpryan]

That could certainly be real. Perhaps there's an enhancer in the deleted gene, or it deletes a TAD boundary, or something along those lines. If you really wanted, you could simulate things to double check that there's no a priori expectation of mucked up read alignment. I wouldn't bother though.