Genomics regions that common to atleast 10 cell types

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4.5 years ago

rohitsatyam102 ▴ 920

Hi Everyone!

I have 142 .bed files related to various cell types that are in standard bed format and contains coordinates. I have been recently tasked to figure out which regions are common in at least 10 cell types. I am perplexed about how to achieve that. Because let's say if we intersect a bed file with 10 different bed files and say 9th bed file has altogether different coordinates while rest of the files have highly overlapping regions, such regions won't come up because those regions are absent from 9th bed file.

Please help!

bedtools bedops genome bed sequence • 749 views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 4.5 years ago by rohitsatyam102 ▴ 920

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Maybe you could tackle this task by generating a huge bed file with all coordinates stated in your 142 bed files. And then go from there? Maybe intersecting the huge file with all 142, if thats possible?

ADD REPLY • link 4.5 years ago by caggtaagtat ★ 1.9k

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Isn't bedtools multiinter meant to be used for this? Why does it have to be 10?

ADD REPLY • link 4.5 years ago by GenoMax 147k

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My boss asked me to take "at least 10" criteria. Bedtools multiintersect does help but how to fulfil at least criteria?

ADD REPLY • link 4.5 years ago by rohitsatyam102 ▴ 920

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