* Being new to alternative splicing analysis jungle, what strategy/program(s) could you experts recommend knowing that, working on human, we have only 1 RNA-seq sample with the matched exome dataset (no replicates)? Is it at least possible?
I read so many reviews and tutorials, and heard about so many programs but they seem to be mainly able to handle differential analysis (replicates or different conditions). The only ones that seem to fit in my case would be splice-aware mappers (to only detect junctions) and maybe SpliceR, SplAdder, CASPER.
* Also, I don't really understand the difference of output you can obtain from programs that reports splicing events only compared to the ones that produce isoforms only (although some can perform both - e.g. SOLAS, MISO, ALEXA-Seq which require multiple samples though). Do the former detect the type of splicing (SE, RI, ...) but don't give you the actual transcripts obtained from the event or you are still able to identify the transcripts?