Calculating p-value for introns which are retained (or not) between 2 conditions I am trying to calculate p-values and ultimately FDR values for RI introns for 2 conditions of experiment I have(control and knockdown)

For every condition I have 3 biological replicates each: 3 control replicates and 3 knockdown replicates.

This is the header line of my input file.

chrom   Istart  Iend    strand  avg-L_R_counts-1    Sk_counts-1 avg-L_R_counts-2    Sk_counts-2


-1 and -2 are 2 sample conditions control and knockout respectively

avg-L_R_counts = for a particular intron, this is the average of reads 5bp up stream and downstream of the 5' end and at the 3'end of the intron

Sk_counts = This is the number of reads spanning exon-exon junction for that intron.

I have approximately 350 introns(this is yeast). I can get the Percent Spliced In values but I am interested in getting a p-value and then I can calculate the FDR values.
Can anyone point me as to what approach I should take to calculate a p-value, or what test should I use?
Here is how we do this:

First break your gene model down into non-overlapping chunks, such that any possible gene model can be built from a combination of those chunks. E.g.

transcript 1 |&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;|----------|&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;|---|&gt;&gt;&gt;&gt;|
transcript 2 |&gt;&gt;&gt;&gt;&gt;&gt;|-------------|&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;|---|&gt;&gt;&gt;&gt;|
transcript 3 |&gt;&gt;&gt;&gt;&gt;&gt;|-------------|&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;|
chunks       |+++1++|+2|+++++3++++|+++4++++|+5+|+6++|


this can be achieved using cgat gtf2gtf --method=genes-to-unique-chunks from the cgat-apps toolkit if you don't want to code it yourself.

I call
chunks 1, 4 and 6 constitutive exon
chunk  3 constitutive intron
chunk  2 alternate intron
chunk  5 annotated retained intron.

Now use featureCounts to count the number of reads in each chunk.

Test the chunk counts for usage using DEXSeq. 

Filter the results to just include chunks of type 2, 3 and 5 and recompute the FDRs.