I am counting reads from rna-seq with htseq-count using a gtf file of enhancer regions, therefore, I want to see how much rna is transcribed from the enhancer.

My problem is that the amount of counts is very low and I obtain a count table like this:

My supervisor is telling me to do a binary table like this, where I have to do the mean (?) of my counts and then establish different column count thresholds and just check if my enhancer is over that value (1) or not (0). Then I have to compare this data with a known enhancer clasification vector with 0 and 1 and see the best coincidence between my rna data and this vector

But always my best count threshold is on the extreme values (count_0 or count_max) so I guess I am not doing something correctly

What could I do?