The -s option isn't working for me with bedtools (v2.17.0). As a test I made two files each with only one line:
file1.bed
file2.bed
Then used this command:
And it reports no overlap. If I run the same command without the "-s" at the end it reports the overlap. Am I missing something obvious?
file1.bed
Code:
chr1 100 200 name1 0 +
Code:
chr1 100 200 name2 0 +
Code:
bedtools intersect -a ./file1.bed -b ./file2.bed -s
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