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Bedtools intersect A contains B and vise versa
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21 months ago
Medhat 8.3k
Texas

Is there is any options when using

bedtools intersect -a A.bed -b B.bed

to detect if line in A contains line in B and vice verse "I do not know if -f could help me in this!!"

for example

A.bed

chr1 100 200

chr1 150 300

B.bed

chr1 110 150

chr1 180 350

the result shall be A contains B (assuming I am using -wb )

chr1 100 200 chr1 110 150

sequence bedtools • 1.1k views
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What is the expected output ?

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the result shall be A contains B (assuming I am using -wb )

chr1 100 200 chr1 110 150

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17 months ago
PoGibas 4.8k
Vilnius
# minimal overlap fraction
# bedtools intersect **-f**
bedtools intersect -b B.bed -a A.bed -wo -f 1​

chr1 110 150 chr1 100 200 40

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Thanks but it does not work like that , I think the one that will work is,

-a b.bed -b a.bed -wo -f 1

chr1 110 150 chr1 100 200 40

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