name of solexa output file

[mchaisso]

Simple question: What is the type of file, or name of the file that contains sequences and qualities in the following format:


@SLXA-EAS1_89:2:1:829:348/2
AACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGC
+SLXA-EAS1_89:2:1:829:348/2
cccccccccccccccccc^c^c^cccbcWcZccZc


thanks,
-mark

[mchaisso]

Simple question: What is the type of file, or name of the file that contains sequences and qualities in the following format:


@SLXA-EAS1_89:2:1:829:348/2
AACTGTATTTTTCTTTCTGCGAGTTAACGCGTTGC
+SLXA-EAS1_89:2:1:829:348/2
cccccccccccccccccc^c^c^cccbcWcZccZc


thanks,
-mark

never mind, FASTQ

[SillyPoint]

I would clarify one thing:

By strict definition (I think), a fastq file contained base quality scores in the phred-style representation: -10*log(E), where E is the probability of a mis-call, converted to an ascii character by adding 33 (so Q40 comes out as 'I').

The base quality scores produced by the Illumina pipeline software (in its *_sequence.txt files) are encoded differently. "Solexa-style" scores are of the form 10*log(P/(1-P)), where P is the probability of a *correct* call, and are converted to ascii by adding 64 (so Q40 comes out 'h').

The two log formulae are asymptotically equal above Q15 or so. But the different scaling factors will bite the unwary.

In the read you included in your message, the quality scores, mostly c's, appear to be encoded "solexa-style".

--SillyPoint