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Old 05-19-2014, 09:47 AM   #1
Location: San Francisco, CA

Join Date: Aug 2011
Posts: 91
Default multiIntersectBed, or something like this


I'm looking for overlapping regions from 3 (or more) bed files. multiIntersectBed from bedtools does that. However, I also want other features and information from those bed files be printed out. Is there a way to do that?
multiIntersectBed shows the regions where the bed files overlap, but it does not include any features from the original bed files.

If anyone knows a solution, I'd greatly appreciate it.

lethalfang is offline   Reply With Quote
Old 05-20-2014, 10:16 AM   #2
Location: Canada

Join Date: Dec 2013
Posts: 62

You might be able to use the regular Bedtools intersect which allows you to output the original entries and pipe the output to another Bedtools intersect. In other words, you'd intersect files 1+2 then intersect the result of that with 3.

Otherwise you could script something with Perl or Python and have complete control over what gets output.
biocomputer is offline   Reply With Quote

bed, bedops, bedtools

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