On Tue, Oct 18, 2011 at 9:02 AM, arabidopsis <svinekod@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