Further to the OP's original question:

The _seq.txt file is just as cgb says: lane, tile, X, Y, sequence. X & Y are in pixels relative to the upper left corner of each tile image, with +X to the right, and +Y down (don't ask).

The _sig2.txt also file starts with lane, tile, X, Y. The rest is intensities for each base, each cycle. Intensities have been corrected for crosstalk and phasing. Pay attention here: For each cycle, there are four values (a,c,g,t). They are separated by *blanks*. Cycles (4 values) are in turn separates by *tabs*.

The _prb.txt file contains base probabilities arranged the same way. No lane/tile/x/y here, though. The probabilities are given Solexa-style: Q = 10 * log (P/(1-P)), where P is the probability that the base is a/c/g/t. Not to be confused with phread-style scores, encoded as Q = -10 * log (E), where E is the probability of an *incorrect* call.

Having said all that, I'm moved to enquire: Why are you looking at what are really intermediate data files? The end product of the pipeline for most purposes is the _sequence.txt files produced by the Gerald step. There you will find what amounts to fastq-format files, containing sequence and base scores, plus lane/tile/X/Y. Only beware that the scores are Solexa-style and encoded as ascii by adding 64 (so Q40='h'). maq expects a true fastq file, with phred-style scores plus 33 (Q40='I').

The _seq.txt file is just as cgb says: lane, tile, X, Y, sequence. X & Y are in pixels relative to the upper left corner of each tile image, with +X to the right, and +Y down (don't ask).

The _sig2.txt also file starts with lane, tile, X, Y. The rest is intensities for each base, each cycle. Intensities have been corrected for crosstalk and phasing. Pay attention here: For each cycle, there are four values (a,c,g,t). They are separated by *blanks*. Cycles (4 values) are in turn separates by *tabs*.

The _prb.txt file contains base probabilities arranged the same way. No lane/tile/x/y here, though. The probabilities are given Solexa-style: Q = 10 * log (P/(1-P)), where P is the probability that the base is a/c/g/t. Not to be confused with phread-style scores, encoded as Q = -10 * log (E), where E is the probability of an *incorrect* call.

Having said all that, I'm moved to enquire: Why are you looking at what are really intermediate data files? The end product of the pipeline for most purposes is the _sequence.txt files produced by the Gerald step. There you will find what amounts to fastq-format files, containing sequence and base scores, plus lane/tile/X/Y. Only beware that the scores are Solexa-style and encoded as ascii by adding 64 (so Q40='h'). maq expects a true fastq file, with phred-style scores plus 33 (Q40='I').

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