Salmon TPM calculation constant
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Entering edit mode
3 months ago
Jjbox ▴ 40

Hi all, salmon seems to calculate the TPM using the equation below, and looks like the constant is 26.1 for every calculated TPM. Does anybody know what this constant means and how it's derived?

TPM = constant * NumReads / EffectiveLength,

salmon TPM • 367 views
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3 months ago
Rob 6.1k

The salmon TPM calculation is

TPM_i = 10^6 * [ (NumReads_i / EffectiveLength_i) / (sum_j (NumReads_j / EffectiveLength_j)) ]


Where NumReads_i is the expected number of reads arising from transcript i, EffectiveLength_i is its effective length, and likewise for j. Can you say how you are deriving this constant of 26.1? Are you looking over _all_ transcripts in the resulting quant.sf file? That number should (barring machine precision) sum to 1,000,000.

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My guess is that its 10^6/(sum_j (NumReads_j/EffectiveLength_j))?

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Entering edit mode

Hi Rob, you are correct. It does sum up to 1M. Thanks a lot. Since you are expert in this tool, could you also help me answer this question here? Intron retention gene expression using salmon