Bedtools -s (strandedness) not working

[biznatch]

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

chr1	100	200	name1	0	+

file2.bed

chr1	100	200	name2	0	+

Then used this command:

bedtools intersect -a ./file1.bed -b ./file2.bed -s

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?

[GenoMax]

$ bedtools intersect -s -a ./file1.bed -b ./file2.bed

That seems to work. Guess options need to go before the the first file entry.

[biznatch]

That seems to work. Guess options need to go before the the first file entry.

Tried that already, it also doesn't work.

[GenoMax]

Tried that already, it also doesn't work.

It works for me. What OS are you using?

$ bedtools intersect -s -a ./file1.bed -b ./file2.bed
chr1	100	200	name1	0	+

$ more p1.bed
chr1	100	200	name1	0	-
chr1	100	200	name1	0	+
$ more p2.bed
chr1	100	200	name2	0	+
$ bedtools intersect -s -a ./p1.bed -b ./p2.bed
chr1	100	200	name1	0	+
$ bedtools intersect -s -v -a ./p1.bed -b ./p2.bed
chr1	100	200	name1	0	-

[biznatch]

I think I figured it out. I'm using bedtools in an Ubuntu virtual machine but saved the files in Notepad++ in Windows. I think it's a newline character problem so the "+" at the end of the line isn't being read correctly. When I made new files in gedit they worked.

[GenoMax]

Easy to overlook that possibility. Good to hear it is working.