FPKM to raw count conversion
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:
Where the ๐_๐ are raw read, ๐_๐ is feature (transcript) length, and โ๐_๐ 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!
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If someone's only giving you FPKMs, I'd be more concerned that they're using some outdated software to align and quantify your RNA-seq reads.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.