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Table 1 RNASEG results on simulated data

From: Transcript mapping based on dRNA-seq data

   a F-measure Recovered sequencing data [%]
  u   1 10 100 1,000 1 10 100 1,000
t = 1 (170 h)   1 0.93 0.93 0.93 0.93 100.00 100.00 99.95 97.92
  10 - 0.93 0.92 0.93 - 100.00 99.96 98.10
  100 - - 0.86 0.86 - - 99.91 99.12
  1,000 - - - 0.67 - - - 97.73
t = 100 (156 h)   1 0.93 0.93 0.93 0.92 100.00 100.00 99.96 98.63
  10 - 0.93 0.92 0.92 - 100.00 99.96 98.10
  100 - - 0.86 0.86 - - 99.91 99.12
  1,000 - - - 0.67 - -   97.73
t = 1,000 (110 h)   1 0.87 0.86 0.83 0.81 100.00 99.98 99.83 97.76
  10 - 0.86 0.83 0.81 - 99.98 99.83 97.76
  100 - - 0.82 0.80 - - 99.81 97.76
  1,000 - - - 0.67 - - - 97.75
  1. F-measure and fraction of recovered sequencing data from the secondary library (in %) for simulated data. RNASEG was applied to the forward strand of region 684,676 to 987,046 of the H. pylori genome. We set k ̂ = 20,000, cp ̂ = 1,000, w = 100, and varying values for parameters t, a and u. We define: True positives (TP) are genes that are part of a transcript segment, true negatives (TN) are intergenic regions that are not part of a transcript segment, false positives (FP) are intergenic regions that are part of a transcript segment and false negatives (FN) are genes that are not part of a transcript segment. ‘-’ indicates parameter combinations that have not been tested because they are not sensible. Numbers in brackets below t correspond to the average runtime in CPU hours for all simulations with this value of t.
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