Answers.Body: <p>According to the book you mentionned <a href="https://www.academia.edu/12825649/Introduction_to_Genomics_Second_Edition-_Arthur_M_Lesk" rel="nofollow noreferrer">Introduction to Genomics SecondEdition by Arthur MLesk</a> p.113</p>
  
  <pre><code>(a) What fraction of a genome could you expect to assemble from eightfold coverage? 
  (b) What total gap length would you expect in an assembly of a 2 Mb target genome size from eightfold coverage? 
  (c) How many gaps would you expect in an assembly of a 2 Mb target genome size from an eightfold coverage of fragments with a read length of 500? 
  (d) You want to sequence a 4 Mb genome by the shotgun method, by assembling random fragments with read length 500. What coverage would you require, to expect no more than four gaps, assuming no complications arising from repetitive sequences or far-from-equimolar base composition?
  </code></pre>
  
  <p>I'm agreed that whitout knowing <span class="math-container">$ N $</span> it's not obvious to answer this last question so perhaps they're a mistake in the statement of this exercise.
  As Devon Ryan suggested, let's assume <code>eightfold coverage</code> means the coverage <span class="math-container">$ C $</span> = 8X</p>
  
  <p>So we can calculate the number of <em>reads</em>:</p>
  
  <p><span class="math-container">$ N = \frac{GC}{L} $</span></p>
  
  <p><span class="math-container">$ N = \frac{4000000\times{8}}{500} = 64000 $</span> <em>reads</em></p>
  
  <p>Then we can calculate the required coverage to expect no more than four gaps:</p>
  
  <p><span class="math-container">$ N( e^{-C}) = 4 $</span></p>
  
  <p><span class="math-container">$ e^{C} = \frac{N}{4} $</span></p>
  
  <p><span class="math-container">$ C = log{\frac{N}{4}} $</span></p>
  
  <p><span class="math-container">$ C $</span> = 10X</p>
  
  <p>(PS: I would like to thank @LordOfRacoons to help answer this question.)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-04T13:08:13.820Z
Answers.LastActivityDate: 2019-10-04T13:14:52.417Z
Answers.LastEditDate: 2019-10-04T13:14:52.417Z
Answers.UserDisplayName: Pierre-Edouard Guerin
Body: <p>I was came across a problem during an exercise in a book and I don't really know how to solve it. I feel like something's missing.</p>
  
  <p>"coverage, c = <span class="math-container">$NL/G$</span> (N=number of reads, L=read length, G=genome length)
  total expected gap length = <span class="math-container">$G(e^{-c})$</span>
  total number of gaps = <span class="math-container">$N(e^{-c})$</span></p>
  
  <p>Question: You want to sequence a 4 Mb genome by the shotgun method, by assembling random fragments with read length 500. What coverage would you require, to expect no more than four gaps, assuming no complications arising from repetitive sequences or far-from equimolar base composition?"</p>
  
  <p>The answer from the book is basically just: Solve <span class="math-container">$N(e^{-c})=4$</span> for <span class="math-container">$c$</span>, but the question doesn't give what <span class="math-container">$N$</span> is? </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-15T12:35:59.523Z
Comments.Text: What do you mean? Isn't N the number of reads? That's what you say in your question.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-15T12:44:19.977Z
Comments.Text: yeah, what I meant was that the question doesn't give me the value of N, without which I can't solve for c
Comments.UserDisplayName: keniji88
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-15T22:00:08.517Z
Comments.Text: Solving for N and solving for C are the same thing (you know L and G in the first equation after all). It also doesn't give you a nice answer because the actual value (11,926,375 reads, which is ~14.9X coverage) isn't really a nice pretty number.
Comments.UserDisplayName: Devon Ryan
Tags: <ngs><genome><assembly><coverage><homework>
Title: Coverage required
ThreadText: # Coverage required
  
  (Asked by: username_0 on 2019-09-15)
  
  I was came across a problem during an exercise in a book and I don't really know how to solve it. I feel like something's missing.
  
  "coverage, c = $NL/G$ (N=number of reads, L=read length, G=genome length)
  total expected gap length = $G(e^{-c})$
  total number of gaps = $N(e^{-c})$
  
  Question: You want to sequence a 4 Mb genome by the shotgun method, by assembling random fragments with read length 500. What coverage would you require, to expect no more than four gaps, assuming no complications arising from repetitive sequences or far-from equimolar base composition?"
  
  The answer from the book is basically just: Solve $N(e^{-c})=4$ for $c$, but the question doesn't give what $N$ is?
  
  **Tags:** ngs, genome, assembly, coverage, homework
  
  > **Comments:**
  > **username_1**: What do you mean? Isn't N the number of reads? That's what you say in your question.  
  > **username_0**: yeah, what I meant was that the question doesn't give me the value of N, without which I can't solve for c  
  > **username_2**: Solving for N and solving for C are the same thing (you know L and G in the first equation after all). It also doesn't give you a nice answer because the actual value (11,926,375 reads, which is ~14.9X coverage) isn't really a nice pretty number.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-10-04. Score: 1
  
  According to the book you mentionned [Introduction to Genomics SecondEdition by Arthur MLesk](https://www.academia.edu/12825649/Introduction_to_Genomics_Second_Edition-_Arthur_M_Lesk) p.113
  
  ```
  (a) What fraction of a genome could you expect to assemble from eightfold coverage? 
  (b) What total gap length would you expect in an assembly of a 2 Mb target genome size from eightfold coverage? 
  (c) How many gaps would you expect in an assembly of a 2 Mb target genome size from an eightfold coverage of fragments with a read length of 500? 
  (d) You want to sequence a 4 Mb genome by the shotgun method, by assembling random fragments with read length 500. What coverage would you require, to expect no more than four gaps, assuming no complications arising from repetitive sequences or far-from-equimolar base composition?
  
  ```
  
  I'm agreed that whitout knowing $ N $ it's not obvious to answer this last question so perhaps they're a mistake in the statement of this exercise.
  As username_2 username_2 suggested, let's assume `eightfold coverage` means the coverage $ C $ = 8X
  
  So we can calculate the number of *reads*:
  
  $ N = \frac{GC}{L} $
  
  $ N = \frac{4000000\times{8}}{500} = 64000 $ *reads*
  
  Then we can calculate the required coverage to expect no more than four gaps:
  
  $ N( e^{-C}) = 4 $
  
  $ e^{C} = \frac{N}{4} $
  
  $ C = log{\frac{N}{4}} $
  
  $ C $ = 10X
  
  (PS: I would like to thank @LordOfRacoons to help answer this question.)
  
  
  ---
  
  