On Mon, May 14, 2012 at 9:03 PM, Claudia Gottstein
<gottst...@cnsi.ucsb.edu> wrote:
> Hi,
> I would like to understand which parameters, ideally which algorithm go into
> the scores one obtains from the quality statistics out of fastQ illumina
> data.
> What is this score composed of? And how come that applying fastq groomer and
> then using fastq summary statistics tool gives a different score as using
> the fast q qc from babraham. I heard fastq groomer may change the data?
>
> EXAMPLE: In my example the scores using fastq groomer and then fastq summary
> statistics were between 3 and 11, whereas using fastq qc straight on the
> data the score was between 32 and 41.
>
> Thank you so much for your explanation.
> Best regards, CG

The Galaxy FASTQ groomer shouldn't change the scores, but
it may change the encoding. Did you read the paper cited in the
tool's help text? http://dx.doi.org/10.1093/nar/gkp1137

See also http://en.wikipedia.org/wiki/FASTQ_format

Peter
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