Divide the genome to vary lengths windows in R
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12 months ago
rrapopor ▴ 30

Hi,

I have BED file with vary windows lengths, and I want to divide the whole genome to non-overlapping bins in same lengths distribution of the BED file in R.

For example, if the chromosome length is 50, and the windows lengths are 10,10,20 , the output should be:

chr1 1 10
chr1 11 20
chr1 21 40
chr1 41 50


Any suggestions?

Thank you!

bedtools R BED • 562 views
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Can you add a representative example?

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These windows are not indexed correctly for the BED format, and are not of the same length distribution.

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12 months ago

You can use bedtools makewindows in R or linux.