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| # merge | |
| bedtools merge -i ifile.bed -c 4 -o collapse # print the merged feature names (4th column) | |
| # intersect | |
| $ cat A.bed | |
| chr1 10 20 | |
| chr1 30 40 | |
| $ cat B.bed | |
| chr1 15 20 | |
| $ bedtools intersect -a A.bed -b B.bed -wa # print only intersecting entry in A.bed | |
| chr1 10 20 | |
| $ bedtools intersect -a A.bed -b B.bed -wa -wb # print both intersecting entries in A.bed and B.bed | |
| chr1 10 20 chr1 15 20 |
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