I had got a Transcriptome Library with 10M PE reads( R1->10M & R2 ->10M ). When I mapped the same to the genes from a particular genome using Bowtie2 80% of them mapped (8M).
Now I need to calculate the Expression rate for these genes. For calculating the FPKM Value I use the formula below
FPKM= MG*(10^9))/N*Length of Gene
MG= Count of PE mapped to the genes (20,000)
N= Library size or Mapped count ?(10M/8M?)
My question is What is the value of N should be is it 10M or 8M