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Table 2 Comparison of reference-depletion screens at different read depths

From: High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

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%
  1. 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.