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  • biocc
    Member
    • Jul 2008
    • 36

    #1

    prhed score

    In fastq file of Illumina 1.3+,quality score = Phred quality +64, which equal solexa quality+64 early, so i should change some code to deal with new solexa data.
    but some calculation is puzzling.

    Given a character $sq, the following Perl code gives the Phred quality $Q:

    $Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10);
    So it is easy to conver Solexa->Sanger quality

    my @conv_table;
    for (-64..64) {
    $conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));
    }
    but i do not understand where is 0.499 from. i think it should be
    conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)))
  • Bio.X2Y
    Member
    • Apr 2010
    • 46

    #2
    It looks like whoever wrote the code just wanted to round the answer to the nearest whole number (since int() on its own always rounds down).

    int(3.1) -> 3
    int(3.5) -> 3
    int(3.9) -> 3

    by adding 0.5 (or in this case 0.499) and then int(), you are rounding to the nearest whole number.

    int (3.9 + 0.5) -> 4

    Not sure why they are using 0.499 instead of 0.5.

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