Bedtools wrongly indicates zero coverage
If this is your output :

chr1    12595   12802   ref|DDX11L1,ref|NR_046018,ens|ENST00000518655,ens|ENST00000450305,ens|ENST00000456328,ens|ENST00000515242  .       ref|DDX11L1     0       0       207     0.0000000


Then I guess your bedfile looks like this (the first 6 fields) :


chrom : chr1
FeatureStart : 12595
FeatureEnd : 12802
name : ref|DDX11L1,ref|NR_046018,ens|ENST00000518655,ens|ENST00000450305,ens|ENST00000456328,ens|ENST00000515242
score : .
strand : ref|DDX11L1


The issue I see here is that you are giving the wrong information to the strand field of your bedfile. It should be either +, either - or . if you don't want to consider the strand information.

Hope it helps !