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Old 03-14-2012, 06:40 AM   #1
Mshegrss
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Default 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.
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Old 03-14-2012, 06:45 AM   #2
HESmith
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Search the forum for 'Illumina quality score' to find the answer.
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Old 03-14-2012, 06:53 AM   #3
Mshegrss
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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.
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