As the IGC matures, we plan on posting tutorials on performing data analysis to help educate Salk researchers. Until we get this effort off the ground, please check out the HOMER next-generation sequencing tutorial as a starting point.
IGC is not a sequencing core. The current focus of IGC is the analysis of genomics data. The NGS core is responsible for the generation of next-gen sequencing data, including library preparation, quantification, and actual sequencing (http://ngs.salk.edu/). However, IGC can help advise groups on their options and coordinate sequencing efforts between multiple groups to help minimize costs.
IGC can offer advice on experimental design, including selection of the appropriate genomics assays, library prep protocols, and sequencing strategies. If your group is new to sequencing, it is a good idea to talk about your plans ahead of time to understand what options are available and to make sure your sequencing plans match the type of data analysis you hope to accomplish after getting your data back.