total reads for ChIP-seq and RNA-seq

Question

[mikysyc2016]

Hi all, When you know the counts number for each gene(RNA-seq) or tags number for each peaks(ChIP-seq), you will need total reads for TPM or RPKM calculation. Which is the right number of total reads? ChIP-seq: (mapped+unmapped) or just mapped reads which one is the right? And how about RNA-seq? Thanks!

Answer 1

[EagleEye]

In any case, only mapped reads should be considered for normalization (as library size).