1 Nov
2011
1 Nov
'11
1:03 p.m.
On Tue, Nov 1, 2011 at 4:58 PM, Kevin Lam <aboulia@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