Question: Values used for calculating FPKM Value
gravatar for bassanio
5.1 years ago by
bassanio20 wrote:

Dear All,

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



bowtie fpkm rpkm • 3.2k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 5.1 years ago by bassanio20
gravatar for geek_y
5.1 years ago by
geek_y11k wrote:

It should be 8M. For example from edgeR rpkm() function, its

lib.size: library size, defaults to ‘colSums(x)’
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by geek_y11k

If I use the same transcript data and alligned with another genome(B) where aligned reads is 9M and then if I do a DeSeq between Sample A(8M) mapped reads and Sample B(9M) mapped reads then the data is Skewed more towards Sample A as the normallization  value is not same between SampleA and Sample

ADD REPLYlink written 5.1 years ago by bassanio20
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