bedtools intersect without range
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6.2 years ago

I have two files:

FileA.bed

ZC3H14    1
VRK1    2
G6PC    79
tp63dn    3
G6PD    174

FileB.bed

ZC3H14    1
VRK1    1
G6PC    14
G6PD    1
tp63dn    2

 

I would like to intersect the two files with bedtools intersect -a FileA.bed -b FileB.bed -loj however, I do not have a range to intersect the two files with. I basically want to print the number in FileB.bed into FileA.bed for the corresponding gene as so:

ZC3H14    1    1
VRK1    2    1
G6PC    79    14
tp63dn    3    2
G6PD    174    1

However, when I try the bedtool command as above, I get an error. Can I not use bedtools for this type of intersection?

P.S. I need the -loj because there are some instances in FileA.bed that are not in FileB.bed, however I still want the line in FileA.bed to print.

 

bedtools intersect • 1.5k views
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use linux join command.

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Perfect. Thank you.

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