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.cock@googlemail.comwrote:
On Tue, Oct 18, 2011 at 9:21 AM, arabidopsis svinekod@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.