Answers.Body: <p>In genetics normally one gets a copy (allele) of a gene (or actually a chromosome) from each parent. If the alleles differ between parents, for example by a SNP, one would have one copy of each allele. With (NGS) sequencing you would get an even amount of reads for both copies. However with somatic mutations, hence mutations which occur after meiosis and gamete forming, one can lose or gain parts of the chromosome (copy number variation). In this situation, some genomic regions might be deleted or amplified. So the allele of one parent can be deleted, leaving you with only the allele of the other parent.</p>
  
  <p>As requested, I have made a simple drawing of a situation where a region differs between parent alleles with SNPs. After a deletion of one of the allele only reads of the other allele are left.
  <a href="https://i.sstatic.net/AMmw3.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/AMmw3.jpg" alt="enter image description here"></a>   </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-28T13:17:08.207Z
Answers.LastActivityDate: 2018-05-28T23:00:05.863Z
Answers.LastEditDate: 2018-05-28T23:00:05.863Z
Answers.UserDisplayName: benn
Body: <p><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0439-6" rel="nofollow noreferrer">In this paper</a>, the authors talk about <em>copy number neutral reads</em> (as reads that equally represent parental chromosomes) and <em>active reads</em> (as reads from only one parent chromosome):</p>
  
  <blockquote>
    <p>We reasoned that the reads mapped into a genomic window can be partitioned in two sets: one set includes reads that equally represent parental chromosomes (copy number neutral reads); and the other set contains reads from only one parent chromosome (active reads).</p>
  </blockquote>
  
  <p>Nonetheless, I have some difficulties understanding these two concepts. Can somebody try to expand on what they wrote?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-28T12:01:19.790Z
Comments.Text: Hard to answer this question, because it is not clear what you don't understand about the two concepts. Do you know what reads are? Chromosomes? I mean it is hard to guess at what level you get lost here.
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-28T12:07:44.747Z
Comments.Text: A drawing of a genomic segment, with some reads mapped to it highlighting which are considered neutral and which active would be appreciated. Thanks.
Comments.UserDisplayName: wrong_path
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-28T12:29:29.257Z
Comments.Text: So your question should be: "Can anyone make a drawing of a genomic segment, with some reads mapped to it highlighting which are considered neutral and which active?"
Comments.UserDisplayName: benn
Tags: <ngs><genomics><cancer>
Title: Difference between copy number neutral reads and active reads
ThreadText: # Difference between copy number neutral reads and active reads
  
  (Asked by: username_0 on 2018-05-28)
  
  [In this paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0439-6), the authors talk about *copy number neutral reads* (as reads that equally represent parental chromosomes) and *active reads* (as reads from only one parent chromosome):
  
  > We reasoned that the reads mapped into a genomic window can be partitioned in two sets: one set includes reads that equally represent parental chromosomes (copy number neutral reads); and the other set contains reads from only one parent chromosome (active reads).
  
  Nonetheless, I have some difficulties understanding these two concepts. Can somebody try to expand on what they wrote?
  
  **Tags:** ngs, genomics, cancer
  
  > **Comments:**
  > **username_1**: Hard to answer this question, because it is not clear what you don't understand about the two concepts. Do you know what reads are? Chromosomes? I mean it is hard to guess at what level you get lost here.  
  > **username_0**: A drawing of a genomic segment, with some reads mapped to it highlighting which are considered neutral and which active would be appreciated. Thanks.  
  > **username_1**: So your question should be: "Can anyone make a drawing of a genomic segment, with some reads mapped to it highlighting which are considered neutral and which active?"  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-05-28. Score: 1 | Accepted answer
  
  In genetics normally one gets a copy (allele) of a gene (or actually a chromosome) from each parent. If the alleles differ between parents, for example by a SNP, one would have one copy of each allele. With (NGS) sequencing you would get an even amount of reads for both copies. However with somatic mutations, hence mutations which occur after meiosis and gamete forming, one can lose or gain parts of the chromosome (copy number variation). In this situation, some genomic regions might be deleted or amplified. So the allele of one parent can be deleted, leaving you with only the allele of the other parent.
  
  As requested, I have made a simple drawing of a situation where a region differs between parent alleles with SNPs. After a deletion of one of the allele only reads of the other allele are left.
  [![enter image description here](https://i.sstatic.net/AMmw3.jpg)](https://i.sstatic.net/AMmw3.jpg)
  
  
  ---
  
  