Is FPM the only normalisation method recommended for CircRNAs?

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!

rna-seq circrna normalisation

• 1,680 views • link

updated 6.2 years ago by Kevin Blighe

• written 6.2 years ago by mimA •

1 answer

Hey,

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

Kevin

• 0 views • link

written 6.2 years ago by Kevin Blighe

More posts like this

Why employ normalization methods, and how can they be utilized in DEG analysis?
written 2.5 years ago by wyt1995 •

I have learned that normalization methods such as CPM (counts per million mapped reads), TPM (transcripts per million), FPKM (fragments per kilobase of transcript per …
Blog: How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression
written 3.4 years ago by Novogene •

Why do mRNA expression values need to be normalized? The unification of mRNA expression value measurements across studies, or the normalization of mRNA data, is …
Normalisation for single nuclei RNA-seq
written 5.0 years ago by MutationalMeltdown

For single cell RNA-seq the typical workflow includes a (log) normalisation step to account for variable sequencing depth. E.g. In Scanpy/Seurat, CPM (Counts per million) …
Investigating expression of potentially autonomous TEs identified.
written 6.1 years ago by lukhanyomakhabane •

Hello guys, I am planning to do expression of autonomous TEs families that I identified in genome of interest. This how I was planning to …
FPKM values from normalized read counts
written 8.2 years ago by Bioin •

Hi Biostars, I would like to get FPKM values from normalized read counts for that I am using this formula FPKM(Fragments Per Kilobase per Million) …
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
written 8.9 years ago by Renesh

In RNA-seq gene expression data analysis, we come across various expression units such as RPM, RPKM, FPKM and raw reads counts. Most of the times …
TCGA/GDC FPKM vs FPKM-UQ
written 9.4 years ago by igor

GDC provides RNA-seq quantification in multiple forms: > For mRNA-Seq data, the GDC generates gene level and exon level > quantification in Fragments Per Kilobase …
Which Expression Units To Use, Fpkm Or Rpkm ?
written 13.3 years ago by biorepine

Dear Biostars! I think this is one of the common problems (which expression units to use, FPKM or RPKM) in RNA-Seq expression analysis. People who …
Raw Counts From Cufflinks Output
written 13.5 years ago by Ge •

Hi, I want to ask how to get the raw counts from the output of cufflinks. One way to do this is to use the …
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
written 15.4 years ago by User 5402 •

Hello, Perhaps this has already been answered somewhere, but I am not seeing a satisfactory explanation. I want to understand how one calculates FPKM (fragments …