...

Standard output of mapping performed by the quantification step includes raw read counts and scaled read counts for every gene and transcript for each sample. The scaling method currently applied is reads per kilo-base of exon model per million mapped reads (RPKM) (Mortazavi et al. Nat Methods 2008). It scales the abundance estimates using exon length and millions of mapped reads and is calculated according to the formula below.

FORMULAImage Added

For example, suppose a transcript has 50 reads that map to it, with an exon transcript length of 7000 bp ( = 7.0 kbp), and there are 5,000,000 reads in that sample. The RPKM value is:

...