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  • Mshegrss
    Junior Member
    • Mar 2012
    • 4

    #1

    Illumina quality score encoding for galaxy grooming

    Hi all,

    To do fastq grooming on galaxy, I have to choose fastq input format, either Illumina 1.3-1.7 or Sanger, for reads done on HiSeq 2000 using GAPipeline vRTA1.10.36. A quality sample from the end of a 210 base read:
    6;95;6HHHHHHHHHHHHHHHHHHHHHHHHHHFHFFHHFFFHFFHHHFFFH>?AA>#@<?##

    If anyone can help me understand which input format to select, much abliged.
  • HESmith
    Senior Member
    • Oct 2009
    • 512

    #2
    Search the forum for 'Illumina quality score' to find the answer.

    Comment

    • Mshegrss
      Junior Member
      • Mar 2012
      • 4

      #3
      It appears that the low quality rating "#" may indicate that this is Illumina 1.8, or "Sanger" in galaxy. However, RTA version 1.10.36 appears to be an old one. Also, nowhere do I have quality scores of I or J. So I'm confused, even after reading up.

      Comment

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