WANI Dictionary

FPKM, fragments per kilobase million

Fragments per kilobase million (FPKM) is a unit of quantify paired-end RNA-seq data.

Using FPKM, gene expression levels are represented in terms of the number of mapped RNA fragments per kilobase of transcript or exon per million mapped reads.

FPKM is calculated using the equation:

The unit of “Length of transcript” is number of base. A specific exon can be used instead of a transcript. See Reference [1] for details.

Other commonly used units to quantify RNA-seq data include transcripts per million (TPM) and reads per kilobase million (RPKM, used for single-end RNA-seq data).

Definitions in the literature

• FPKM stands for fragments per kilobase of exon per million mapped fragments. It is analogous to RPKM and is used specifically in paired-end RNA-seq experiments [1].
• Count up the total reads in a sample and divide that number by 1,000,000 – this is our “per million” scaling factor; Divide the read counts by the “per million” scaling factor. This normalizes for sequencing depth, giving you reads per million (RPM); Divide the RPM values by the length of the gene, in kilobases. This gives you RPKM [2].

Some references, including the above Reference [2], use “Total number of reads in sample” instead of “Total number of mapped reads”. This appears incorrect according to reliable references such as [1].