<p>Currently, I am trying to analyze some CAGE data from the FANTOM5 consortium (<a href="http://fantom.gsc.riken.jp" target="_blank">fantom.gsc.riken.jp</a> and for the data <a href="http://fantom.gsc.riken.jp/5/data/" target="_blank">http://fantom.gsc.riken.jp/5/data/</a>).</p>

<p>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?<br />
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 &quot;activity&quot; of an enhancer is related to eRNA abundance.</p>

<p>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?<br />
<br />
It would be great if you can help me here.</p>

CAGE detects promoters of coding and lncRNA, miRNA promoters, post-transcriptionally processed RNAs, eRNA and so on.

1. If you want to process CAGE BAM files yourself, here is the tool: http://www.ncbi.nlm.nih.gov/pubmed/25653163

2. CAGE detects post-transcriptionally processed RNA signals spread across exons, and they have very different characteristic features, here is the paper: http://www.ncbi.nlm.nih.gov/pubmed/24002785

3. CAGE detects miRNA promoters along with Drosha processing events, described here: http://www.ncbi.nlm.nih.gov/pubmed/26673698

In general, CAGE tags detected at the promoter is mRNA abundance, that is used to quantify gene expression level. CAGE tags at the promoters show nice correlation with RNA-seq. You can also read the Fantom5 papers itself.