On the Analysis of Optical Mapping Data - University of Wisconsin ...
On the Analysis of Optical Mapping Data - University of Wisconsin ...
On the Analysis of Optical Mapping Data - University of Wisconsin ...
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Figure<br />
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3.5 Parametric models for µ(M) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45<br />
3.6 Comparison <strong>of</strong> significance strategies using iterative assembly . . . . . . . . . . 48<br />
3.7 LR scores for ungapped global alignment . . . . . . . . . . . . . . . . . . . . . . 50<br />
3.8 Optimal scores vs self-alignment score . . . . . . . . . . . . . . . . . . . . . . . 52<br />
3.9 Self-score plot for simulated data . . . . . . . . . . . . . . . . . . . . . . . . . . 54<br />
3.10 Thinning <strong>of</strong> coverage in optical map alignments . . . . . . . . . . . . . . . . . . 55<br />
3.11 Estimated thinning rates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56<br />
3.12 Effect <strong>of</strong> permutations on test statistics . . . . . . . . . . . . . . . . . . . . . . 59<br />
4.1 Power function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64<br />
4.2 Results <strong>of</strong> one simulation run . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68<br />
4.3 Summary <strong>of</strong> several simulation runs . . . . . . . . . . . . . . . . . . . . . . . . 69<br />
4.4 The GM07535 genome compared to CHM . . . . . . . . . . . . . . . . . . . . . 71<br />
4.5 Results for MCF-7 chromosomes 17 and 20 . . . . . . . . . . . . . . . . . . . . 73<br />
5.1 Correlation <strong>of</strong> sizing errors within map . . . . . . . . . . . . . . . . . . . . . . . 78<br />
5.2 Improvement in optimal alignment score . . . . . . . . . . . . . . . . . . . . . . 79