In RNA-seq data analysis, what is the advatage of using FPKM over normalizing reads of a feature (such as gene) by the length of the feature?

15 August 2013 1 4K Report

Using FPKM seems to be misleading when the treated sample has massive changes in gene expression.

FPKM means fragment per kilobase of exon model per million reads sequenced. Fragment is an insert, for example a 2 paired-end reads account as 1 fragment.

FPKM is a double-normalization. It normalizes by transcript length and also by the total number of fragments sequenced. It is important to normalize also by the total number of fragments sequenced because different RNA-Seq libraries could have different sizes, which affects the amount of fragments mapped to each transcript.

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