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  • different Illumina convention in fastq files?

    We have a few different Illumina data sets here, and I'm wondering if there has been a change in the characters used in fastq files, or that we have just been given bad data.

    we have some sequences for which the translation works fine:
    10*log(1+10**(c - 64/10.0))/log(10)

    @SLXA-EAS1_89:3:1:715:750/1
    GTCTTGAAAGCTATGATGTCAAGATTAATTTAATC
    +SLXA-EAS1_89:3:1:715:750/1
    bbbbbbbbbbbbbbbbb^bbbbbbbbbbbbbbbba
    @SLXA-EAS1_89:3:1:747:756/1
    GTGTATTGCTCAATCTTCGAACGGGGGGAGGATTG
    +SLXA-EAS1_89:3:1:747:756/1
    bbbbb^bbbbbbbbbbbbbbbbbbbbbb\bbObbb
    @SLXA-EAS1_89:3:1:859:343/1
    GTTAATAGATTTAATTGCCACCGCAATACCAGCAA
    +SLXA-EAS1_89:3:1:859:343/1
    ccccccccccccccccbcccccccbbbbbbbYbb^

    However we have other sequences where the quality is 10 or below using the same translation. Is one using Sanger center convention and the other Illumina?

    @ILunknown_unknown_1_1_107_394
    TATTCCCCGCCCCCCCGTCGTGCCCGGTCTTTGTCC
    +
    IIIIIIGI/<I8IIIIII.II//I);II)%<>III&
    @ILunknown_unknown_1_1_118_376
    TTGGGAAGCGCACCCGGCCCGTGTTGGCTTTCGCCT
    +
    I%I!I(,@+I"%",!#&)"5$'&$&%$.*%$"#"""
    @ILunknown_unknown_1_1_342_174
    GCGGCGGGTTATCGGGGCACTCCCCCCCTCCCGCAC
    +
    IIIIII2I<#?II+@CI1/CI0III5%(5'I%0-%$
    @ILunknown_unknown_1_1_121_440
    TGGCGTCCAGGCCGGCCTGGCTGCCGTCCGGCCCCC
    +
    II50I5I.&-*+9-&>2$&&3#&#"#%%"&"#&#&&
    @ILunknown_unknown_1_1_109_530
    TTTGCGTTAGGTAAAATGCTAGAAGCAGGTGAGCAG
    +
    IIIIIIIIIIIIIIIIIIIIIII&II0IIII%II0A

    thanks,
    -mark

  • #2
    The top is illumina/solexa format (what you would see in s_[1-8]_sequence.txt) and the bottom is the fastq Sanger format.

    To convert solexa values
    perl -e 'my $qual = 10 * log(1 + 10 ** ((ord($myChar) - 64) / 10.0))/log(10); print int($qual);'

    To convert fastq values
    perl -e 'my $qual = ord($myChar) -33; print $qual;'

    hope that helps

    Comment

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