Hi!,
I have problems with bedintersect.
I need to intersect two bed files like these:
A.bed
chr1 10568 10571 - 5
chr1 10568 10571 - 5
chr1 10568 10571 - 5
chr1 10568 10571 - 5
chr1 11804 11900 + 2
chr1 11804 11900 + 2
chr1 11804 11900 + 2
chr1 11804 11900 + 2
chr1 16720 16745 + 2
chr1 16720 16745 + 2
B.bed
chr1 11373 12727 NR_046018 DDX11L1 + Ex1*
chr1 11873 12227 NR_046018 DDX11L1 + Ex1
chr1 12112 13221 NR_046018 DDX11L1 + Ex2*
chr1 12227 12612 NR_046018 DDX11L1 + In
chr1 12612 12721 NR_046018 DDX11L1 + Ex2
chr1 12720 14909 NR_046018 DDX11L1 + Ex3Last*
chr1 12721 13220 NR_046018 DDX11L1 + In
if I run this line:
intersectBed -a A.bed -b B.bed -s -c >out
it return an empty file; If I run:
intersectBed -a A.bed -b B.bed -c >out
it return a file with the overlapping coordinates.
Any suggestions for this problem?
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