Intron retention events for a condition sample with 3 replicates I have 3 biological replicates of RNA seq data for a particular condition. I want to find out intron retention events from those biological replicates for a given condition. There is no comparison I am doing here. Just from the three replicates, I am trying to find out what introns are retained in my sample. There is only one condition here. Tools like rMATS require 2 conditions. Is there any tool I can use to find out intron retention events given that I only have one condition (with replicates).

Ideally I would like to use a method similar to that used in this paper, though I can't fully grasp their methodology. This would allow me to get p-values for enrichment of specific introns.
All introns will have some level of retention and I guess no intron will be 100% retained. In the absence of a comparator, you will need to work out how much intron retention an intron needs to be called retained. This is a human judgement, there is no automated way of deciding this. 

What you need to do this is some sort of PSI calculation (percent-spliced-in). MISO will provide this, but it doesn't do replicates, so I guess you'll need to run it on each sample and then average the PSIs and determine if it surpasses some sort of threshold you have set.