On Tue, Nov 1, 2011 at 4:58 PM, Kevin Lam <aboulia(a)gmail.com> wrote:
actually Illumina 1.8+ has one more quality value higher than
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.