Question: Finding downstream Gene Closest To A Given Location
0
gravatar for PAn
2.0 years ago by
PAn20
United States
PAn20 wrote:

Hi,

I am trying to find genes closest only downstream to a bed file. I am using

bedtools closest -d  -a Seq.bed -b Bed_GTF_neg.bed

but it is giving me both upstream and downstream regions, is there anyway to get only the downstream regions?

Thanks!

closest bedfile gene bedtools • 1.1k views
ADD COMMENTlink modified 2.0 years ago by harold.smith.tarheel4.2k • written 2.0 years ago by PAn20
3
gravatar for harold.smith.tarheel
2.0 years ago by
United States
harold.smith.tarheel4.2k wrote:

From the BEDtools 'closest' webpage:

-iu = ignore upstream

ADD COMMENTlink written 2.0 years ago by harold.smith.tarheel4.2k
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