what is the latest version of bedtools and can you please provide a download? Thanks.
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Let me google that for you.
2.16.2
Go here:
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Bed_intersect -s empty output
Hi,
I try to use bed intersect to intersect two bed files using -s parameter.
a.bed
b.bedHTML Code:chr1 11804 11900 + 2 0 1 0 3 23 0 0 0 0 4 2 1 0 1 15 0 0 0 0 17 3 00 0 1 0 0 1 1 0 1 8 0 1 1 0 4 4 0 5 0 0 0 1 0 0 2 1 00 0 0 3 0 0 0 0 1 0 0 0 0 4 0 0 2 0 0 0 0 9 0 0 3 0 00 0 5 2 0 0 0 0 1 0 3 2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 01 0 0 0 0 0 0 0 5 7 2 0 2 2 2 0 chr1 11804 11900 + 2 0 1 0 3 23 0 0 0 0 4 2 1 0 1 15 0 0 0 0 17 3 00 0 1 0 0 1 1 0 1 8 0 1 1 0 4 4 0 5 0 0 0 1 0 0 2 1 00 0 0 3 0 0 0 0 1 0 0 0 0 4 0 0 2 0 0 0 0 9 0 0 3 0 00 0 5 2 0 0 0 0 1 0 3 2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 01 0 0 0 0 0 0 0 5 7 2 0 2 2 2 0 chr1 11804 11900 + 2 0 1 0 3 23 0 0 0 0 4 2 1 0 1 15 0 0 0 0 17 3 00 0 1 0 0 1 1 0 1 8 0 1 1 0 4 4 0 5 0 0 0 1 0 0 2 1 00 0 0 3 0 0 0 0 1 0 0 0 0 4 0 0 2 0 0 0 0 9 0 0 3 0 00 0 5 2 0 0 0 0 1 0 3 2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 01 0 0 0 0 0 0 0 5 7 2 0 2 2 2 0
If I use -s parameter bed intersect return an empty file, but if I remove the -s parameter it return a non empty file with some strand match.HTML Code: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
Any idea?
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