From TopHat 2 alignment, I have obtained outputs containg splice junctions and the corresponding read counts. I am interested in calculating differential splice junction usage between wild type and mutant samples.
In a recent publication (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358997/ ), the DEXSeq function called "testForDEURT" was used to quantify differential splice junction usage between two samples. However, I am not able to figure out the important steps to use this function.
I have wild type and mutant samples in replicates, and therefire some statistics, for example, p-value and FDR, will be needed to define signficantly candidates.
Could somebody please guide me doing this analysis. Any response is highly appreciated.