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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

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    $\begingroup$ Why don't you ask the individual who gave that advice instead of asking others to interpret it? $\endgroup$
    – user3051
    Feb 23, 2020 at 14:19
  • $\begingroup$ Thank you, I emailed him but he did not reply me back $\endgroup$
    – Angel
    Feb 23, 2020 at 16:44

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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.

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