I suggest that anyone conducting some genome-scale analysis should start with Galaxy. The creators describe it as a "web-based data analysis framework that allows you to collect and work with biological data from many different sources". I have been using it for some time, mainly for one-off analyses or to prototype something I plan to implement in a pipeline (to see whether it is worthwhile). It interacts with UCSC genome browser as well as the EnsEMBL ENSMART/BioMart system to get data, though you can also upload your own data if you want. Try it, and It would be good to have some user feedback posted here as well.