Quantify ration of spliced to unspliced reads

[wespiser]

Hello,
I am interested in measuring the ratio of spliced to un-spliced genes in an RNA-seq experiment. Is there a method/technique/tool that can do this on the transcript or gene level?
Thank you
Adam

[dpryan]

I'm not aware of a tool geared toward that, but doing the measurement wouldn't be terribly difficult. Firstly, to annotate each gene as spliced or not just load your annotation GTF/GFF into R and make a GRanges out of that. Then split() by gene_id, reduce(), and lapply() a function that returns, say, 1 if length(x)>1 and 0 otherwise. You then have list of 0s and 1s for unspliced and spliced genes. For the metric, you'd want RPKMs or FPKMs, for which cufflinks might be a wise choice here (I'd normally suggest just calculating those yourself, but the method used by cufflinks should be superior for your needs).