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

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Default multiIntersectBed, or something like this

Hi,

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?

https://www.biostars.org/p/13516/
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.

Thanks.
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Old 05-20-2014, 10:16 AM   #2
biocomputer
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Default

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.
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