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  • Bed to BedGraph

    Hi everyone..

    I am interested in converting the bed file to bedgraph file. Any help or advice will be highly appreciated.

    Thanks

  • #2
    Hi,
    Maybe this helps : http://groups.google.com/group/bedto...3754383fbe24b7

    Comment


    • #3
      Hi,
      I install bedtools and invoke
      ./genomeCoverageBed -bg -trackline -trackopts name=${new} -i $file -g sizeMouse.txt > ${new}.bedgraph
      Lana

      Comment


      • #4
        This command solved my problem.

        Originally posted by schaffer View Post
        Hi,
        I install bedtools and invoke
        ./genomeCoverageBed -bg -trackline -trackopts name=${new} -i $file -g sizeMouse.txt > ${new}.bedgraph
        Lana

        Comment


        • #5
          Originally posted by schaffer View Post
          Hi,
          I install bedtools and invoke
          ./genomeCoverageBed -bg -trackline -trackopts name=${new} -i $file -g sizeMouse.txt > ${new}.bedgraph
          Lana
          What genome file is that? I have ChIP-seq data that I'm trying to visualize in Bedgraph format. I tried using the human.hg19.genome provided by bedtools as my genome file but got the error: The requested genome file (human.hg19.genome) could not be opened.

          Comment

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