I hope this actually leads to a few answers, but I have RNASeq data and I want to study alternative splicing/isoform switch between two conditions.
I'm not sure what tools to use, but I have done transcript quantification with Kallisto. The results are on a cluster and overall we have 672 samples so it is impossible to move these directories into my personal computer.
My next step is to use Sleuth, however sleuth is in R. How do people use the cluster for quantifying and then use Studio for Sleuth?
Additionally, one other question I have is about using Sleuth for Alternative Splicing. I believe that Sleuth is not the best for Alternative Splicing and that I should use IsoformSwitchAnalyzeR instead. Which is also on R.
My second question mainly is: Can sleuth be used for Alternative Splicing or is it just for DGE?