actually Illumina 1.8+ has one more quality value higher than fastqsanger
(see http://en.wikipedia.org/wiki/FASTQ_format )

my question now I guess is if I use fastqsanger would it break anything
when it encounters the 'J' in the qual values?

On Tue, Oct 18, 2011 at 5:10 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Tue, Oct 18, 2011 at 9:21 AM, arabidopsis <svine...@gmail.com> wrote:
> > If Illumina 1.8+ is already using the Sanger FASTQ encoding, the file
> should
> > be recognized by downstream applications, like Quality statistics
> computer,
> > quality filter etc. However, my file is not visible by those programs and
> > when I click on it, only "uploaded fastq file" is displayed, without
> > encoding details.
> >
> > S.
>
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