I would like to get FPKM values from normalized read counts for that I am using this formula FPKM(Fragments Per Kilobase per Million) = [# of fragments]/([length of transcript]/1000)/([total reads]/10^6)
My problem is in gtf file most of the geneids having more than one transcript with different lengths. I am confused which one to consider for my calculation.
Any comments will be helpful for my analysis.
Thanks in advance.