How to translate RNA-Seq result to normalized gene expression level in qRT-PCR?

[ymc]

In the qRT-PCR world, they use "cycles to threshold" (Ct) to measure expression level. Usually they pick one gene as reference and then use it to normalize expression of other genes. The normalized gene expression equals Ct_ref - Ct_gene.

If I want to do similar thing with RNA-Seq, how do I do it? I learned that HTSeq cannot be used for this purpose because reads mapping to region that is shared by multiple genes will be discarded due to ambiguity. So HTSeq is good for DE analysis but not for getting normalized gene expression level. Is there other read counting tool that can do what I want?

Thanks a lot in advance!