Table 2

Comparison of reference-depletion screens at different read depths

Total reads

Depletion

Min FPR

FNR


10 million

25%

0.00%

49.95%

10 million

50%

0.00%

2.89%

10 million

75%

0.00%

0.00%

5 million

25%

3.41%

42.35%

5 million

50%

0.02%

1.28%

5 million

75%

0.00%

0.00%

2.5 million

25%

9.65%

49.95%

2.5 million

50%

1.70%

1.07%

2.5 million

75%

0.00%

0.00%


The false positive and false negative rates at a range of log ratio thresholds were calculated by comparing each depletion group to the non-depleted hairpins after filtering to exclude hairpins with low representation (<100 raw reads) in the reference set. The minimum false positive rate (Min FPR) found is shown along with the associated false negative rate (FNR). We were able to consistently detect a 50% depletion in hairpin representation using a total of only approximately 2.5 million reads.

Sims et al. Genome Biology 2011 12:R104   doi:10.1186/gb-2011-12-10-r104

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