7.2 years ago by
Santiago de Compostela, Spain
genome coordinates are always the same, it's you who decide whether to move in the increasing or in the decreasing direction. if you have already split your bedfile into positive and negative strand coordinates, and considering that the positive strand moves from 5' to 3' and that upstream is strictly moving in the 5' direction, if you are interested in upstream only windows you should use the -l (left coordinates) option with posStrand.bed and the -r (right coordinates) option with negStrand.bed. the -sw option is just a way of defining the same window to the left and to the right at the same time, which is not what you're looking for.