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  • Bedtools -s (strandedness) not working

    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
    Code:
    chr1	100	200	name1	0	+
    file2.bed
    Code:
    chr1	100	200	name2	0	+
    Then used this command:
    Code:
    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?

  • #2
    $ bedtools intersect -s -a ./file1.bed -b ./file2.bed
    That seems to work. Guess options need to go before the the first file entry.

    Comment


    • #3
      Originally posted by GenoMax View Post
      That seems to work. Guess options need to go before the the first file entry.
      Tried that already, it also doesn't work.

      Comment


      • #4
        Originally posted by biznatch View Post
        Tried that already, it also doesn't work.
        It works for me. What OS are you using?
        Code:
        $ bedtools intersect -s -a ./file1.bed -b ./file2.bed
        chr1	100	200	name1	0	+
        Code:
        $ 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	-
        Last edited by GenoMax; 10-07-2013, 02:35 PM.

        Comment


        • #5
          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.
          Last edited by biznatch; 10-07-2013, 02:42 PM.

          Comment


          • #6
            Easy to overlook that possibility. Good to hear it is working.

            Comment

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