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Table 1 Number of nucleosomes identified on simulated data by different methods at three levels of coverage

From: ChIPseqR: analysis of ChIP-seq experiments

   ChIPseqR GeneTrack MSP MTC WTD
3 M reads Sample 1 8,386 8,386* 4,809 0 0
  Sample 2 8,299 8,299* 4,726 0 4
  Sample 3 8,388 8,388* 4,892 0 0
  Total 25,073 25,073* 14,427 0 4
  % stable 24.9% 4.7% 5.4% - 25%
  repeatability 0.07 0.02 0.007 - -
6 M reads Sample 1 6,257 6,257* 7,968 0 0
  Sample 2 6,286 6,286* 7,912 0 0
  Sample 3 6,431 6,431* 8,139 0 0
  Total 18,974 18,974* 24,019 0 0
  % stable 52.7% 6.7% 6.5% - -
  repeatability 0.16 0.05 0.014 - -
10 M reads Sample 1 19,907 19,907* 9,989 542 142
  Sample 2 20,359 20,359* 9,951 621 143
  Sample 3 20,223 20,223* 9,851 545 192
  Total 60,489 60,489* 29,791 1,708 477
  % stable 32.5% 18.2% 7.7% 68.1% 48.8%
  repeatability 0.31 0.16 0.06 0.10 0.04
  1. *Cut-off was chosen to give the same number of significant predictions as ChIPseqR.
  2. For each sample the number of predicted nucleosomes is reported. The total number of significant predictions for each level of coverage is reported together with the proportion of stable nucleosomes that were identified in all three samples as well as a measure of repeatability of stable nucleosome predictions between samples (see text for details).
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