I have used rMATS to get the output files of various types of alternative splicing, and then what should I do next? I want to count the types of splicing of each file. I don't know what software to use?
If what you want is to compare different conditions and look for differences in splicing you should focus on the differential splice sites (as identified by rMATS) since the vast majority of splice sites will not be changing whereby counting to total number of sites will not be a particular sensitive approach.
If you are interested in obtaining a genome wide summary of changes between conditions we have recently developed a statistical approach for this which you can get a quick idea of what it can do in this part of the IsoformSwitchAnalyzeR vignette as well as read the article here. If you have any questions for this please don't hesitate to ask.
If you want to just count number of AS events in each sample, you have to run these sample again themselfs. For exemples, b1.txt and b2.txt should both been:
the PSI scores will obviously be equal to 0 but by counting the number of rows (and thus events) in each of the 5 result files for the 5 types of possible events (A3SS,A5SS,RI,MXE,SE), you will have the number of associated splicing events for the sample in question