Question: Get overlapping features with certain fraction max
gravatar for irfanwustl
23 days ago by
irfanwustl20 wrote:

Hi, Given two bed files, I want to get the overlapping feature which has at most x bp overlap. Probably I should use closest bed but how to restrict the overlap to some x bp at most?

bedtools genome • 103 views
ADD COMMENTlink modified 23 days ago by Pierre Lindenbaum134k • written 23 days ago by irfanwustl20
gravatar for Pierre Lindenbaum
23 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

pipe the output of bedtools intersect into awk to filter on the overlapsize:

awk '{x1=int($2);x2=int($5);B=x1<x2?x2:x1; x1=int($3);x2=int($6);E=x1<x2?x1:x2;if(E-B<20) print}'
ADD COMMENTlink written 23 days ago by Pierre Lindenbaum134k
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