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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/