Confusion With Illumina Version And Phred Scores
Hi there,
I received some old Illumina datasets to analyse that were generated using "GAPipeline-1.5.1" (that's what I read on the report file...). From what I guessed it means the quality scores are "Illumina 1.5 encoded", ie Sanger-type. Am I right ?
Sorry if the question sounds a but dumb ....
1 answer
Illumina 1.5+ data does not use Sanger encoding (Phred+33). Have a look here for a description. If you are unsure about the encoding, FastQC will tell you which encoding you have (there may be other/better methods). If you need to convert your data to Sanger encoding, I recommend using the seqret tool from EMBOSS as it is faster than the BioPerl/BioPython methods in my experience.
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