TPKM vs FPKM

Question

[nanoide]

Hello, so I have a simple question I hope anyone can clarify I've seen some papers presenting RNA-seq data in TPKM, but I'm not sure on what does this mean. Is this the same than FPKM?

Thanks for your time

[Kevin Blighe]

Never heard of TPKM. Do you mean TPM?

[nanoide]

I am aware of the differences between FPKM/RPKM and TPM. I had never heard of TPKM either. It seems it's used by some few papers. For example, this scholar search. I would say it's used as FPKM but I wanted to be sure.

[Istvan Albert]

the search results are amusing - or hair-raising depending on your disposition.

It looks like in most cases it is just a misunderstanding and misquotation. In some cases FPKM in others TPM is stated as TPKM. There is one case there that seems to define TPKM as on-target per kilobase mapped reads but that appears to be no different than RPKM - the definition of "mapped reads" is replaced with "on target reads" -

[h.mon]

There is another definition, found at a dissertation: tags per kilobase of pre-miRNA per million CLIP-seq reads. Funnily enough, TPKM is defined at a figure legend, and never used in the main text.

[Kevin Blighe]

Strange............

[nanoide]

Thank you, now I think I got a pretty good idea that is not a common term, I'll make sure to recheck where my data's coming from. Thanks!

Answer 1

[Istvan Albert]

My favorite resource still:

• What the FPKM? A review of RNA-Seq expression units

[nanoide]

Thanks for the source, it's alway good to refresh these concepts

Answer 2

[ATpoint]

Check StatQuest. Even comes with a video.