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  • How to convert eland file to BED format

    I have file in the following format. I want to use MACS but it requires bed format how can I convert my file to bed format

    HWUSI-EAS230-R 1 2 4 713 1086 0 1 ACAAGTTACATAACCTCCCTGATATTATGAACCCAA aaabaaab`baaa``aa_`aa`aaaaaaaaa\^_`a c3.fa 188833058 R 36 118

    Thanks,

  • #2
    The following awk script converts sorted file to BED format that has 4 fields. You can update the script as you need...

    # sortedToBed.awk
    # Input : SORTED FILE
    # Output : <Chromosome> <start position> <stop position> <strand>
    # Usage
    # awk -f sortedToBed.awk SORTED_INPUT_FILE_NAME > BED_OUTPUT_FILE_NAME

    {OFS=" ";

    len=length($9);

    split($11, ref_chr, ".");

    if ($13=="F") strand = "+";
    else if($13=="R") strand = "-";
    else strand = "None";

    if (strand!="None")
    print ref_chr[1], $12, $12+len, strand ;
    }


    Good Luck!
    Selen

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