Thread: Ion Proton Q20
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Old 11-05-2013, 01:39 AM   #7
Location: Singapore

Join Date: Sep 2010
Posts: 27

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.

Just by looking at the data in a browser you can see many more artifacts the lower the QScore but i agree, it is difficult to compare all these apples and oranges and bananas, as with changing read length, PE vs SR, long reads from Pacio the final assembly/alignment will show you stats which might look comparable at first sight but once you drill down deeper it raises many questions...
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