Get common segments from several segment files
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18 months ago
heskett ▴ 110

Hi all! I have a bunch of CNA segment files from multiple samples and want to compare them, problem is all the segments have different start and stop sites in each sample. Is there a one liner pre-built tool to get a new list of segments that covers all the segments from each sample? For example see drawing:enter image description here

copy-number • 646 views
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18 months ago

look at bedtools multiinter

 $ bedtools multiinter -header -i a.bed b.bed c.bed -names A B C
 chrom  start   end num list    A   B   C
 chr1   6   8   1   A   1   0   0
 chr1   8   12  2   A,C 1   0   1
 chr1   12  15  3   A,B,C   1   1   1
 chr1   15  20  2   A,B 1   1   0
 chr1   20  22  1   B   0   1   0
 chr1   22  30  2   A,B 1   1   0
 chr1   30  32  1   B   0   1   0
 chr1   32  34  1   C   0   0   1
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i think this is it!

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Okay I looked into it Pierre. This counts the number of files that have segments at each location, but it doesnt report features at each interval that I am interested in like copy number in this example. But I guess it does give the intervals that I want, so i could then do some kind of bedtools map or bedtools intersect to get the CN values from each file after that. thanks

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