ratio mRNA:pre-mRNA in total RNA-seq data

Question

[JindrichK]

Hi,

I would like to quantify the ratio of pre-mRNA vs mRNA for each gene in a total RNAseq dataset.

I have read a few papers that says it can be done, but with no informations on how.

So far, I've mapped my reads to the genome, and used featureCounts to get:

• mRNA counts (-exon grouped by megafetaure -gene_id)

• whole gene (- gene grouped by megafeature -gene_id)

The difference should be whatever mapped to introns and thus some measure of pre-mRNA level. BUT theres an issue with what number I can actually compare (normalised for length? of total introns? )

Is there a better way?

Thanks!