FPKM to raw count conversion

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3.8 years ago

Dominik • 0

Hi!

Since I am new in bioinformatics I was wondering if it is possible to convert FPKM values into raw counts. Unfortunately I don't have an access to the raw counts but I have information about the transcript lengths (from ensambl data base) and information about number of total reads. And since FPKM is expressed as: enter image description here

Where the 𝑞_𝑖 are raw read, 𝑙_𝑖 is feature (transcript) length, and ∑𝑞_𝑗 corresponds to the total number of mapped reads, is it correct (from bioinformatics point of view) to just calculate q_i from this formula to end up with raw counts?

Thank you for help!

rawcounts RNA-seq FPKM DEG • 3.7k views

ADD COMMENT • link updated 3.8 years ago by dsull ★ 7.8k • written 3.8 years ago by Dominik • 0

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Entering edit mode

If someone's only giving you FPKMs, I'd be more concerned that they're using some outdated software to align and quantify your RNA-seq reads.

Furthermore, the l_i in FPKM is not transcript length, it's the "effective length" which is different than the transcript length. You likely don't have the effective length (it's not something you can get from ensembl because it's sample-dependent).

Just get the raw FASTQ data and process it yourself.

ADD REPLY • link 3.8 years ago by dsull ★ 7.8k

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