Closed:BEDtools multiinter merges non-overlapping intervals
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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?

BEDtools multiinter • 552 views
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