sort suitable overlap base by using bedtools intersect

Question

[mikysyc2016]

When I use bedtools intersect funtion how i can sort which have 10 bases or longer overlap in overlap.bed? what kind of command i can enter?

Answer 1

[Alex Reynolds]

If you want to require a minimum threshold of overlap between elements in reference and map sets, you could do the following:

$ bedops --element-of 10 reference.bed map.bed > answer.bed

The file answer.bed will contain elements in reference.bed which overlap elements in map.bed by ten or more bases.