Calculate complete Splicing Index (coSI) for exons

Question

[aditi.qamra]

Hi,

I was trying to calculate a splicing index for exons as done in this paper.

A schematic for the same is

I am not sure how to calculate this index specially with extremely limited knowledge of dealing with RNAseq data but I;m thinking on the lines of using junction information from TopHat output junctions.bed and then exon coordinates from Refseq and the reads ofcourse from the bam files and overlapping them to get a-e.

Has anybody calculated this before ?

Thanks!

[Pierre Lindenbaum]

duplicate of Calculate Percent Spliced In (PSI) ?

[aditi.qamra]

Looks like it - Will go through the above post. Clearly I wasn't searching with the right keywords. Thanks !

[william.ackerman.729035]

coSI looks to be a different metric that PSI? Why is e in both the numerator and denominator?