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 what way would you typically use the 2 in combination?
Specially, when you find alternative intronic promoters from CAGE, you can can ask if the CAGE detected 5'-end is supported by RNA-seq 5'end. You can also correlate how CAGE tags from CDS with RNA-seq. CAGE tags originating in promoters or introns or CDS have different initiator sequence, that can be very useful to make sense of your data. Please read the paper: http://www.ncbi.nlm.nih.gov/pubmed/24002785