I have been using bedtools for a long time but I can't seem to quite figure the following operation. Hope someone can help!
cat test.bed chr1 5 27 chr1 7 12 chr1 10 20 chr1 22 27 chr1 24 30 bedtools merge -i test.bed chr1 5 30
Now I wish to conduct something that would like :
# first two lines chr1 5 6 1 #only shown once chr1 7 10 2 #shown twice
I can do it with coverage option by showing the base depth option, but surely there may be something that is even quicker!