On Tue, Nov 1, 2011 at 4:58 PM, Kevin Lam <abou...@gmail.com> wrote:
> 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?

The Sanger FASTQ format has always allowed J (PHRED 41), the
issue is some tools might treat that as an error as it is unusually
high for a raw read. For instance, you need at least FASTX v0.0.13
to cope with this - older versions didn't like it.
http://seqanswers.com/forums/showthread.php?p=49667

Peter
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