Appropriate application of RPKM

Question

[Joshi]

Hi,

Would appreciate any advice on this particular topic... Having seen examples of RPKM calculations and what they signify - I'm not entirely clear whether it's an appropriate metric for exome sequencing coverage.

From what I understand, it's appropriate when trying to compare relative transcript expression (in an RNA Seq experiment) between two samples or test conditions... That analogy clearly doesn't apply to exome sequencing. With that in mind; is there any instance where carrying out RPKM type calculations for exome sequencing output makes sense?

Thanks for your help, Himanshu

Answer 1

[Damian Kao]

The only reason I can think of why you would want to calculate coverage for your exome sequencing is to evaluate the pull down efficiency of your probes.

[WouterDeCoster]

Another would be to assess the possibility of structural variations and using the coverage as a proxy for the number of fragments in your initial sample prep.