I am looking for a piece of software that can be used to investigate alternative splicing and fulfills the following four criteria:
- can handle more than two experimental conditions
- breaks AS events down by type (e.g., cassette exon, mutually exclusive exons, alternative 5’ splice site, alternative 3' splice site, intron retention)
- can be used in rat
- AS events can be mapped back to protein sequences
I am having a surprising amount of difficulty identifying a tool that meets these criteria. Exon-based tools like DEXSeq, diffSplice, or JunctionSeq can be used to analyze more than two groups, but cannot readily distinguish between different types of AS events. Conversely, among the event-based tools I have investigated, two (MISO and VAST-TOOLS) do not seem to be available for rat, one (rMATS) seems to only handle two-group comparisons, and one (MAJIQ) returns very complex events that I am having quite a lot of difficulty mapping to protein sequences.
Is there a method I am not aware of that could be used to identify alternative splicing events in rat in an experiment with three conditions?
Thanks in advance for your help.