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.


On Tue, Oct 18, 2011 at 10:12 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Tue, Oct 18, 2011 at 9:02 AM, arabidopsis <svine...@gmail.com> wrote:
> > Hi all,
> >
> > Fastq groomer has Solexa or Illumina 1.3+ as an input quality format. I
> > asked at the sequencing facility about their machine and output and they
> > said their format was Illumina 1.8+ (the newest). I tried to convert my
> > fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an input
> > option and got all reads with quality of around 10... Does it mean that
> > Galaxy cannot be used on a dataset with 1.8+ encoding or something
> > else was wrong?
> >
> > Thanks,
> >
> > Slon
> Illumina 1.8+ is already using the Sanger FASTQ encoding, so you
> don't need to convert it with the groomer.
> I think the Galaxy team might still recommend it as it doubles as
> a sanity test for corrupt FASTQ files.
> Peter
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