What sort of pipeline would you recommend on doing RNA-seq exon-level analysis for about 100 samples?
Our goal is study differential exon expression and splicing in our data. We have case and control groups with three time points and our focus is to study how does the exon expression and spicing differ between groups across all timepjoint when accounting for the within sample variability. For gene-level analysis we have used DESeq2 and LRT-testing.
I've looked into DEXseq but with a lot of sample is seems to be really computationally too demanding. Other option that we've considered have been diffSplice in limma and diffSplice in edgeR but not quite sure if those are the way to go.
Would really appreciate comments on what would be the best approach to the exon-level data. Is it possible to do LRT-testing with exon-level data with some of these methods?