Re: [bedtools-discuss] multiIntersectBed: Sorting issue? Unable to find the correct overlapping regions

[Aaron Quinlan]

Hi Elizabeth,

This tool expects the chromosomes to be sorted lexicographically, then numerically by start position (sort -k1,1 -k2,2n).  I am on the road at the moment and can't test, but by eye, files d.bed and e.bed appear to violate this criteria.  They should look like:

cat d.bed

22 24119495 24129657

6 162733091 162787714

cat e.bed

22 19940225 20492436

22 20704584 21465947

22 21649054 23280752

22 23280753 24800557

22 24800558 24888638

3 60231378 60335915

4 1534933 2243243

Please try this and let me know if the results make more sense.

- Aaron

quinlanlab.org

On May 3, 2013, at 7:11 PM, Elizabeth Chun <mii...@gmail.com> wrote:

Hello there,

I used the multiIntersectBed tool to find the overlapping regions between 5 BED files below, which has a common region of overlap between chr22:24,119,495-24,126,702 involving 4 BED files.

When I ran multiIntersectBed, I noticed two things: (1) It identified the region of overlap between chr22:24,115,623-24,126,702 involving only 2 BED files; (2) The output was not sorted by chromosome, which prompted me to think that may be it was not sorting the contents of multiple files correctly.

When I create BED files with the entries from chr22 only, then the overlap result looks OK.

Below, I show the contents of all BED files, and how I ran multiIntersectBed tool, and the output file content.

Could you please take a look and let me know what is going on?

Thank you,

Elizabeth

> cat a.bed 

22 24115623 24126702

> cat b.bed 

1 28496 109092

> cat c.bed 

1 564190 569884

22 23057818 23332540

22 23332541 24809382

22 24809383 25035966

> cat d.bed 

6 162733091 162787714

22 24119495 24129657

> cat e.bed 

3 60231378 60335915

4 1534933 2243243

22 19940225 20492436

22 20704584 21465947

22 21649054 23280752

22 23280753 24800557

22 24800558 24888638

> ~/bedtools-2.17.0/bin/multiIntersectBed -header -names a b c d e -i a.bed b.bed c.bed d.bed e.bed > overlap.txt

> cat overlap.txt 

chrom start end num list a b c d e

1 28496 109092 1 b 0 1 0 0 0

1 564190 569884 1 c 0 0 1 0 0

22 23057818 23332540 1 c 0 0 1 0 0

22 23332541 24115623 1 c 0 0 1 0 0

22 24115623 24126702 2 a,c 1 0 1 0 0

22 24126702 24809382 1 c 0 0 1 0 0

22 24809383 25035966 1 c 0 0 1 0 0

3 60231378 60335915 1 e 0 0 0 0 1

4 1534933 2243243 1 e 0 0 0 0 1

22 19940225 20492436 1 e 0 0 0 0 1

22 20704584 21465947 1 e 0 0 0 0 1

22 21649054 23280752 1 e 0 0 0 0 1

22 23280753 24800557 1 e 0 0 0 0 1

22 24800558 24888638 1 e 0 0 0 0 1

6 162733091 162787714 1 d 0 0 0 1 0

22 24119495 24129657 1 d 0 0 0 1 0

============= Testing with BED files with chr22 only ==============

> cat a.bed

chr22 24115623 24126702

> cat b.bed

chr22 23057818 23332540

chr22 23332541 24809382

chr22 24809383 25035966

> cat c.bed

chr22 24119495 24129657

> cat d.bed

chr22 19940225 20492436

chr22 20704584 21465947

chr22 21649054 23280752

chr22 23280753 24800557

chr22 24800558 24888638

> ~/bedtools-2.17.0/bin/multiIntersectBed -header -names a b c d -i a.bed b.bed c.bed d.bed > overlap.txt

> cat overlap.txt 

chrom start end num list a b c d

chr22 19940225 20492436 1 d 0 0 0 1

chr22 20704584 21465947 1 d 0 0 0 1

chr22 21649054 23057818 1 d 0 0 0 1

chr22 23057818 23280752 2 b,d 0 1 0 1

chr22 23280752 23280753 1 b 0 1 0 0

chr22 23280753 23332540 2 b,d 0 1 0 1

chr22 23332540 23332541 1 d 0 0 0 1

chr22 23332541 24115623 2 b,d 0 1 0 1

chr22 24115623 24119495 3 a,b,d 1 1 0 1

chr22 24119495 24126702 4 a,b,c,d 1 1 1 1

chr22 24126702 24129657 3 b,c,d 0 1 1 1

chr22 24129657 24800557 2 b,d 0 1 0 1

chr22 24800557 24800558 1 b 0 1 0 0

chr22 24800558 24809382 2 b,d 0 1 0 1

chr22 24809382 24809383 1 d 0 0 0 1

chr22 24809383 24888638 2 b,d 0 1 0 1

chr22 24888638 25035966 1 b 0 1 0 0

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