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  • Coryza
    Member
    • Feb 2014
    • 29
    #1

    Bedtools - complementBed not working properly

    Hi,

    I have some strange issues with bedtools using the command complementBed (bio-Linux). When running the example.

    A.bed
    chr1 100 200
    chr1 400 500
    chr1 500 800
    my.genome
    chr1 1000
    complementBed –i A.bed –g my.genome

    This should give
    chr1 0 100
    chr1 200 400
    chr1 800 1000
    instead I get
    chr1 0 1000

    Anyone knows how this is possible?
    Tags: bedtools
  • Coryza
    Member
    • Feb 2014
    • 29
    #2
    With all correct indentations & formats (it works @ someone else) I get the error
    "Differing number of BED fields encountered at line: 3. Exiting..."

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