Answers.Body: <p>They created 10kb bins, which could be called "dividing the genome". These are just 10kb long contiguous stretches (so position 1-10000,then 10001-20000, etc.). This is, of course, a nonsensical way of going about things, because "counting those up" in the regions you posted is the same as taking the width of the regions, dividing by 10000, and rounding a bit.</p>
  
  <p>Presumably you have your markers in something like BED format, so just use bedtools to intersect them and do the counting for you.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-23T16:27:04.087Z
Answers.LastActivityDate: 2020-02-23T16:27:04.087Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I have a copy number segment file with this by SCAT R package</p>
  
  <pre><code>Chromosome  Start   End
  1           10583   120983
  1           121009  245455
  1           404187  5719467
  1           5719471 5735807
  </code></pre>
  
  <p>I want to count the number of markers in these locations</p>
  
  <p>I asked somebody how to do this, he replied:</p>
  
  <p><strong>We created marker file by dividing the genome into 10 kb bins, so the markers file contains the start and stop positions for each of these 10kb segments for each chromosome along with ASCAT segments start and end positions. Then, for each ASCAT copy number segment, we count how many markers fall within that region for total probes.</strong></p>
  
  <p>Can somebody helps to understand what he mean by dividing the genome </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-23T16:44:55.447Z
Comments.Text: Thank you, I emailed him but he did not reply me back
Comments.UserDisplayName: Zizogolu
Tags: <r><wgs><cnv>
Title: What does this statement mean?
ThreadText: # What does this statement mean?
  
  (Asked by: username_0 on 2020-02-23)
  
  I have a copy number segment file with this by SCAT R package
  
  ```
  Chromosome  Start   End
  1           10583   120983
  1           121009  245455
  1           404187  5719467
  1           5719471 5735807
  
  ```
  
  I want to count the number of markers in these locations
  
  I asked somebody how to do this, he replied:
  
  **We created marker file by dividing the genome into 10 kb bins, so the markers file contains the start and stop positions for each of these 10kb segments for each chromosome along with ASCAT segments start and end positions. Then, for each ASCAT copy number segment, we count how many markers fall within that region for total probes.**
  
  Can somebody helps to understand what he mean by dividing the genome
  
  **Tags:** r, wgs, cnv
  
  > **Comments:**
  > **username_0**: Thank you, I emailed him but he did not reply me back  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-02-23. Score: 4 | Accepted answer
  
  They created 10kb bins, which could be called "dividing the genome". These are just 10kb long contiguous stretches (so position 1-10000,then 10001-20000, etc.). This is, of course, a nonsensical way of going about things, because "counting those up" in the regions you posted is the same as taking the width of the regions, dividing by 10000, and rounding a bit.
  
  Presumably you have your markers in something like BED format, so just use bedtools to intersect them and do the counting for you.
  
  
  ---
  
  