So a pretty simple question - but when you sequence a chromosome does it have any innate strandedness? Or did someone just decide when DNA came off the sequencer that primer X was binding to the sense strand and primer Y was binding to the antisense strand, and so long as everything else thats mapped is mapped to the right strand, it doesn't really matter what you call sense and antisense?
The reason I ask is that there are gaps in every organisms genome, and surely as soon as you have a gap you don't know if the 'sense' DNA either side of the gap are actually on the same strand. Perhaps in the future when that gap gets filled, you'll find your sense's don't match up.
Does my question make sense? ;-)