Use +1 for match and -1 for mismatch multiplied by base quality scores. OES with +1 for match and -1 for mismatch.(default: use empirical base frequencies) Nevertheless, we observed in practice that for the case the actual overlap sizes are relatively small, test 2 can correctly assemble more reads with only slightly higher false-positive rate.ĭisable empirical base frequencies. Therefore, this is not a valid statistical test and the 'p-value' is in fact the maximal probability for accepting the assembly. However, it assumes that the minimal overlap is the observed overlap with the highest OES, instead of the one specified by -v. This test methods computes the same probability as test method 1. Use the acceptance probability (m.a.p).For example, setting the cut-off to 0.05 using this test, the assembled reads might have an actual p-value of 0.02. Note that due to its discrete nature, this test usually yields a lower p-value for the assembled read than the cut-off (specified by -p).
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