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?