Recently, I am interested in finding common mutation among different batches of samples. But I have not found approaches to determine common alternative splicing and novel transcripts. Any advice about this topic is appreciated. Thank you.
The pipeline Kevin suggest will give you the basis for doing the downstream analysis of acutal splice events.
If you are interested in isoform switches (which enables easy biological interpretation) you can use one of my tool IsoformSwitchAnalyzeR. Alternatively rMATS or DEXSeq can be used to find exon-level differences. Leafcutter lies somewhere in between analyzing clusters of splicing.