Thread: Ion Proton Q20
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Old 11-05-2013, 02:32 AM   #8
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

Originally Posted by Buzz0r View Post
In that case how can you compare the Qscores at all? Clearly, it makes a huge difference if you look at a Illumina Q30 run, a Proton Q17 run or a PacBio <Q10 run.
Evaluating (and comparing) the correctness of Q scores for a well-known dataset is fairly easy -- PhiX is a common one, but everyone has their own pet. All you need to do is to compare the quality values with what is expected ("This is a 17-generation inbred strain with SNPs here, here and here, and a gene translocation from here to here. If the sequence is showing a SNP here, then that's probably an incorrect base").

The generation of Q scores is difficult (think P vs NP if you're a maths person), and that leads to data-specific biases that in most cases cannot be predicted prior to carrying out a run on a new sample.
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