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

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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?

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