I have 12 RNA-Seq samples corresponding to 6 biological replicates each of 2 conditions. Is there an overview of methods for identifying differential splicing from RNA-Seq data? By differential splicing, I don't mean alternative splicing in general, but specific cases in which Condition A uses a particular isoform of a gene and Condition B uses a different isoform of that gene.
I'm aware that Cufflinks (Cuffdiff specifically) performs differential splicing tests. Are there any other documented tools or methods for doing this?