Hello,

I am new to these technologies, and would like some more information to distinguish each. In what ways can CAGE and RNA-seq data complement each other? What is unique for each of the technologies?

For instance, given I have some data that supposedly also has matching CAGE data that is mapped and clustered. If these samples match the RNA-Seq samples, how do I know if the CAGE samples can complement the RNA-Seq analysis?

Thanks for any help!
In CAGE, only mRNA with 5' caps are captured and sequenced. 

Usually there will be multiple TSS for a gene and some genes may have multiple promoters. In RNA-Seq you will get to know which genes/transcripts are expressed, because the mRNA is randomly fragmented and sequenced, but that does not tell the which promoter being used. CAGE-Seq on the other hand, sequences the 5' regions of mRNA, which tells you the precise location of TSS at 1bp resolution, which explains you about the promoter usage and promoter architecture.

In short, if you want to study the promoter architecture, you need to use CAGE "like" data. If you are only interested in expression, RNA-seq would be enough. If you have deep enough the CAGE data, you could study both the promoter architecture and the gene expression.