Transcript Quantification

Note that we use absolute read counts because we are going to compare counts across samples.

Other metrics for comparison of genes within the same sample are:

• CPM (Counts Per Million) Each gene count is divided by the corresponding library size (in millions).
• RPKM (reads per kilobase of exons per million mapped reads)

• TPM (Transcript per Million)

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  1. Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK).
  2. Sum up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor.
  3. Divide the RPK values by the “per million” scaling factor. This gives you TPM

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