How to remove the same genome coordinate in two bed files?

Question

[bright602]

Hi, I have two bed files, say file A and file B.

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File A:

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• chr3 181879479 181879497
• chr3 181879496 181879514
• chr3 181879507 181879525
• chr3 181879555 181879573

---

File B:

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• chr3 181879496 181879514
• chr3 181879507 181879525

---

How can I subtract the common items in A and B from A, and get bed file C as follow

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• chr3 181879479 181879497
• chr3 181879555 181879573

Thanks a lot for your help.

Answer 1

[slw287r]

use the following command to remove intersected `regions' of A and B from A:

bedtools subtract -a A.bed -b B.bed > C.bed

or if you just want to remove the shared `lines' from A:

awk -F'\t' 'BEGIN{OFS="\t"}NR==FNR{a[$0];next}{if(!($0 in a)){print}}' B.bed A.bed > C.bed

Answer 2

[igor]

Try bedtools intersect -v -a A.bed -b B.bed: http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

[bright602]

Thank you, I tried using bedtools, but it turns out lots of item are lost. In the case above, it only shows chr3 181879555 181879573