Entering edit mode
6.6 years ago
ATpoint
81k
I saw the following behaviour of BEDtools multiinter, which is not really what I expected.
cat test1.bed
chr1 1 6
chr1 6 10
#
cat test2.bed
chr2 6 10
#
bedtools multiinter -i *.bed
chr1 1 10 1 1 1 0
chr2 6 10 1 2 0 1
=> Why does the command concatenates the non-overlapping intervals of test1? Splitting test1 into two BEDs and using BEDtools intersect shown no intersection, as it should be. Any ideas how to circumvent this in multiinter?