How do i extract rows from a bedfile that have a certain bedscore?

Question

[a.rex]

I have a typical bedfile - I want to extract out rows that have a read coverage score/bedscore of >100.

Any tips on how to do this would be much appreciated.

Answer 1

[Alex Reynolds]

Assuming five-column BED, with the score or signal in the fifth column:

$ awk '$5>100' in.bed > out.bed

If you're working with a bedGraph file:

$ awk '$4>100' in.bedGraph > out.bedGraph