In order to give a better answer, though, we're going to need more information about what your data consists of and what your goals are.
Here are some good review papers for you to start with, that will help you find out what's possible and what's not. Also, you can make your live with these data much easier using R & Bioconductor.
Some good resources for R where mentioned here.
- Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews. Genetics. 2009;10(1):57-63. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19015660.
- Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nature methods. 2009;6(11 Suppl):S22-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19844228.