I am interested in finding the rpkm values for my genes(exons). The basic definition of RPKM given is :
In the formula for RPKM it's written in the denominator that mapped reads(millions). How can we get this mapped read number.
If i get this from fastq file then i dont think it would be the correct mapped reads , because not all the reads match to the ref genome,or is it.
Hope to hear from you guys soon