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  • epi
    Member
    • Jan 2012
    • 38

    find overlaps/common in multiple bed file

    Does anyway have experience to find commonalies (or overlaps) between bed files. I have 4 bed files and want to find what intervals are common to all.

    And I don't have any rigid criteria for overlap, any intersection will do.

    Appreciate any answers.
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    Have a look at bedtools, specifically the intersectBed utility.

    Comment

    • GenoMax
      Senior Member
      • Feb 2008
      • 7142

      #3
      http://pypi.python.org/pypi/pybedtools is a python extension of the bedtools that was mentioned in the post #2 by dpryan.

      Comment

      • husamia
        Member
        • Apr 2010
        • 66

        #4
        Originally posted by epi View Post
        Does anyway have experience to find commonalies (or overlaps) between bed files. I have 4 bed files and want to find what intervals are common to all.

        And I don't have any rigid criteria for overlap, any intersection will do.

        Appreciate any answers.
        I mentioned the wrong function I meant to mention Galaxy with the Intersect function in the operate on genomic intervals functions
        here is example


        Galaxy is a community-driven web-based analysis platform for life science research.
        Last edited by husamia; 01-23-2012, 07:03 AM. Reason: corrected intersect instead of merege for overlapping bed files

        Comment

        • epi
          Member
          • Jan 2012
          • 38

          #5
          Originally posted by dpryan View Post
          Have a look at bedtools, specifically the intersectBed utility.
          Thanks for response everyone !

          I could implement intersectBed as pairwise. And to find common among 4, I can do multiple pairwise, but it seems there is some chance for false negatives.

          I dint get chance to look at the python script so far, I wonder if that adresses this issue.

          Comment

          • husamia
            Member
            • Apr 2010
            • 66

            #6
            I mentioned the wrong function, I modified my response above to reflect the correct reference function. Sorry for confusion

            Comment

            • dpryan
              Devon Ryan
              • Jul 2011
              • 3478

              #7
              Originally posted by epi View Post
              Thanks for response everyone !

              I could implement intersectBed as pairwise. And to find common among 4, I can do multiple pairwise, but it seems there is some chance for false negatives.

              I dint get chance to look at the python script so far, I wonder if that adresses this issue.
              The python interface isn't very different from direct command line usage and I would suspect produces the same results. I also don't see how you'd get a false negative, provided you actually want regions existing in all of the bed files.

              Comment

              • epi
                Member
                • Jan 2012
                • 38

                #8
                Originally posted by dpryan View Post
                The python interface isn't very different from direct command line usage and I would suspect produces the same results. I also don't see how you'd get a false negative, provided you actually want regions existing in all of the bed files.
                Thanks again for responding. I realize i did not state my objective well enough.
                This is chip-seq analysis for which I have bed files (peaks). There could be a situation when peak 1 intersect peak 3 at 5' and peak 2 intersect peak 3 at 3`. but peak 1 and peak 2 do not intersect.
                Read Peak1, Peak2 and Peak3 coming form Samples 1,2 and 3 please.
                intersectBed will not reveal these peaks on my first paiwise comparison (peak1 and peak2) so it will be gone. Logically, it seems they come from same region so I was wondering if there is a tool that could capture those.

                I must mention that this is not a real example, just i theoretical possibility which crossed my mind. May b I am just too obsessed over it

                Comment

                • mgogol
                  Senior Member
                  • Mar 2008
                  • 197

                  #9
                  You want multiIntersectBed...

                  Comment

                  • arvid
                    Senior Member
                    • Jul 2011
                    • 156

                    #10
                    Originally posted by epi View Post
                    Read Peak1, Peak2 and Peak3 coming form Samples 1,2 and 3 please.
                    intersectBed will not reveal these peaks on my first paiwise comparison (peak1 and peak2) so it will be gone. Logically, it seems they come from same region so I was wondering if there is a tool that could capture those.
                    You can include both A and B regions in the output from intersectBed (e.g. with -wo), merge them with mergeBed and then intersect the merged output to the next sample (to "grow" the overlapping regions).

                    Comment

                    • epi
                      Member
                      • Jan 2012
                      • 38

                      #11
                      Originally posted by mgogol View Post
                      bullseye !!

                      Looks like can the job, will try it out ...
                      appreciate your response

                      Comment

                      • sjneph
                        Junior Member
                        • Jan 2013
                        • 2

                        #12
                        If you prefer a much more scalable solution that can do this simple intersection (and any other set-like operation) on any number of bedfiles at once, check out BEDOPS.

                        Comment

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