Hello

I have WIG file and need to find genes regulated by the protein which is alternatively spliced (to be precise - the type of alternative splicing should be a5ss - alternative donor sites)

Please advise what programs should I use for this purpose.
[MATS][1] is my favorite tool for splicing event analysis

 [1]: http://rnaseq-mats.sourceforge.net/

As mentioned in the previous comment, MISO is another option. In both cases, you need `.bam` files for RNA-Seq data (neither uses ChIP-Seq data, which is probably not a reliable tool for analyzing splicing events).