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Old 08-18-2010, 07:56 AM   #14
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Location: sweden

Join Date: Sep 2009
Posts: 121

No, I implemented a MapQ score: BestScore - 2ndBestScore (I don't divide by total score like you, this seems to improve the accuracy). I then optimized the minimum mapq score (you use a fixed one of 10 I think) per read length and error rate by calculating the lowest score that assures a 99% specificity and then I report the sensitivity with that threshold.
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