Unfortunately, I am not that experienced in analyzing CAGE data. They do provide some processed data for both the TSS expression and enhancers and some processing software. However, I want reprocess these data myself and to start at least with the BAM files. So given CAGE BAM files, what would you suggest to use to get out both a sensible value of gene expression for each TSS (and Isoform) and the same for the enhancers?
For the former, usually I would simply take cuffdiff with some GENCODE annotation, but I am unsure whether this is just sensible for RNA-Seq and not for CAGE - or what would you use for it? And I still have no idea how to do it similarly with enhancers (under the assumption that I am having their annotation) - should I count the number of tags falling into these regions?. Also do you know how the "activity" of an enhancer is related to eRNA abundance.
Generally speaking, should I consider the mRNA abundance for a gene measured with CAGE in FANTOM5 as the level of transcription initiation or the the steady-state mRNA level after posttranscriptional regulation (by miRNAs)? Also are other RNAs like miRNAs or lncRNAs included?
It would be great if you can help me here.