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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
Line 33: Line 33:
   * 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