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Illumina is
over-creative with their own formats.
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.seq.txt:
base-called sequences
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.prb.txt:
qualities for each nucleotide/each cycle (is some kind of semi-raw data?)
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Illumina FASTQ is
not real FASTQ, but looks similarly (to cause confusion). The quality score
is an own Illumina score, computed by subtracting 64 from the ASCII code of
the character. For example the ‘h’ in the example is ord(‘h’) – 64 = 104 – 64
= 40.
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See
http://www.asciitable.com/ for ASCII codes (Dec is the ‘ord’ in decimal
numbers).
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The Illumina score
can be transformed to Phred score. Given a character ch, the following
expression should give the Phred quality q (please double-check:) q = 10 * log(1 + 10 ^ (ord(ch) - 64) /
10.0)) / log(10)
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Qseq: Not looking
like FASTQ, but the scores are proper Phred scores. Their encoding is however
still ASCII – 64.
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Illumina “single
line format” and SCARF: base-called sequences and quality scores in a bit
more handy format.
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