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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