Salmon TPM calculation constant
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,
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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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