Is FPM the only normalisation method recommended for CircRNAs?

Question

[mimA]

Hi all,

I have a question. For circRNAs detected by RNA-seq, I've read various articles suggesting to use FPM (Fragments per million mapped reads) for normalisation of the raw counts. Is it wrong to use FPKM for circRNA normalisation - the difference being FPKM also corrects for the gene length.

Thanks and best!

Answer 1

[Kevin Blighe]

Hey,

Can you cite the sources? FPKM may correct for gene length, but it fails to correct for cross-sample differences.

Kevin