Confusion With Illumina Version And Phred Scores

Question

[Pasta]

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 ....

Answer 1

[SES]

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.

[Pasta]

Thanks mate ;-)