Basically, my goal is estimating neoantigen amount. For this purpose, I think both methods have their advantage and disadvantage
Using DNA for mutation detection ignores the expression information. Not all variant are expressed
By using RNA for mutation detection, we can take expression level into account and give different weight to each somatic mutation on its capability to produce neoantigen. However, one single RNA-Seq only represents the expression at a single time point.
Both of them have bias. I think which methods is better depends on if the gene expression across tumor genome vary significantly.
Any comments are appreciate