I understand from the BED "standard" at UCSC that it is a residue, 0-based, half-open system. And all the examples make sense - on the positive strand.
For example - http://alternateallele.blogspot.de/2012/03/genome-coordinate-conventions.html - is a great post about this.
However for the negative strand - which end is the half-open end? Is it always the largest value or is it the end "not-used"?
I found this link - http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms - to be a hot mess as the numbers are reversed - which is not what I want.
If I'm converting a negative strand gene annotation from GTF to BED - is it always GTF(start,end)--> BED(start-1,end) - even for negative strand?