lecture_notes:03-30-2011

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lecture_notes:03-30-2011 [2011/04/01 12:07] svohr Added notes from coverage discussion. |
lecture_notes:03-30-2011 [2011/04/01 12:20] (current) svohr [Coverage] slight corrections |
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* Useful when mapping to a reference. | * Useful when mapping to a reference. | ||

===== Coverage ===== | ===== Coverage ===== | ||

- | We briefly discussed how much sequence data would be required to assemble the genome. First, we considered the probability of seeing every base | + | We briefly discussed how much sequence data would be required to assemble the genome. First, we considered the probability of seeing a particular base ''i'' in a single read ''j''. |

- | in the genome | + | |

| | ||

P( seeing base i in read j ) = L/G | P( seeing base i in read j ) = L/G | ||

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P( never seeing base i ) = (1 - L/G)^R | P( never seeing base i ) = (1 - L/G)^R | ||

- | We can multiple ''L/G'' by ''R/R'' to get ''((L*R) / G) / R'' or ''C / R'' where ''C'' is our coverage of the genome. We take the limit of this as | + | We can multiply ''L/G'' by ''R/R'' to get ''((L*R) / G) / R'' or ''C / R'' where ''C'' is our coverage of the genome. We take the limit of this as |

''R'' goes to infinity: | ''R'' goes to infinity: | ||

lim n->inf (1 - C/R)^R = e^-C | lim n->inf (1 - C/R)^R = e^-C | ||

- | Thus we can expect to miss G*e^-C bases. | + | Thus we can expect to miss ''G*e^-C'' bases. |

We cannot assemble an entire chromosome if we are missing bases. However, we can construct contiguous stretches of bases or //contigs// and later | We cannot assemble an entire chromosome if we are missing bases. However, we can construct contiguous stretches of bases or //contigs// and later |

lecture_notes/03-30-2011.1301684823.txt.gz · Last modified: 2011/04/01 12:07 by svohr