I have read this post on CAGEseq and RNA-seq ,and about the differences in their protocols.
Also,the paper on their comparison which shows they have similar expression profiles: http://genome.cshlp.org/content/early/2014/03/04/gr.156232.113.long
However,In terms of analysis.
1) Can we use similar tools for CAGE seq as well ? e.g. STAR for alignment and Cufflinks for getting FPKM values , Fusioncatcher for getting the fusions ?
2) Another question is if we have samples from RNAseq as well. Can we compare the CAGEseq samples vs RNAseq samples to do differential expression and clustering?