How To Use Bedtools Windows To Overlap Upstream For Positive Strand Strand

Question

[roll]

Hi,

I am trying to use bedtools windows. It has been explained in the manual of the bedtools but I am still bit confused and thought a confirmation would be good. And I have no biological background.

I have divided my bedfile into two, based on the strand information(For example, posStrand.bed and negStrand.bed).

I would like to screen overlaps of LINEs within 5000bp upstream of my postStrand.bed file.

1. In this case shall I use -l or -r option from bedtools window?
2. since all are on + strand, do I need to use the -sw option?

Answer 1

[Jorge Amigo]

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.

[roll]

thank you, this is great