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  • motif genome wide

    Hi all,

    Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

    Thanks!
    L

  • #2
    It is depends on what kind of motif format do you have
    Homer has a program (findKnownMotifs.pl), which use matrix, but fuzznuc (part of the Emboss package) use consensus sequence as query.

    Comment


    • #3
      @Liy: Just to be clear about what you are asking.

      You know the motif you want to get corresponding coordinates for (genome wide) with output in BED format.

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      • #4
        Originally posted by Liy View Post
        Hi all,

        Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

        Thanks!
        L
        You may download from here http://compbio.mit.edu/encode-motifs/

        Comment

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