Report name of overlapping features using `bedtools intersect`

[Gloria Sheynkman]

I am using bedtools intersect to compare the gene ranges of two databases.

Is there a way to report not only that there exists overlap between a feature, but the name of the features?

In the example, below:

$cat A.bed

chr1 10 20 Gene A

chr1 30 40 Gene B

$cat B.bed

chr1 15 20 Gene A'

Could the output be:

chr1 10 20 Gene A chr1 15 20 Gene A'

Thanks,

Gloria

[Aaron Quinlan]

Hi Gloria,

Certainly. Use the -wa and -wb options together.

Aaron

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[Gloria Sheynkman]

Thank you for the answer - bedtools is a dream.