I want to quantify the leads in my defined region.
This is not a gene, but an enhancer region. (from ENCODE)
The data is a bam file that maps total RNA-seq using tophat.
I want to measure the expression of a region that is thought to be an enhancer RNA that is not defined in human gtf.
So I wondered if I could use the gffs for the regions I want to use for quantification.
But, I am not sure which tool to use and how.