text: user4595: 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 
  
  user77: 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.
  
original_text: 4595: <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>
   77: <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>
  