Question: How To Use Bedtools Windows To Overlap Upstream For Positive Strand Strand
gravatar for roll
6.7 years ago by
United Kingdom
roll320 wrote:


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?
bedtools windows strand • 3.0k views
ADD COMMENTlink modified 6.7 years ago by Jorge Amigo11k • written 6.7 years ago by roll320
gravatar for Jorge Amigo
6.7 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Jorge Amigo11k

thank you, this is great

ADD REPLYlink written 6.7 years ago by roll320
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