Compare a long list of BEDFiles against a whole genome/ chromosome ?
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5.3 years ago
dearbbhyc • 0

Do you think it is possible for me to compare a list of BEDFiles against a whole genome or even chromosome? If so, How?

I am trying to compare a list of chromosomal regions to a whole genome CNV map and then count the number of gains and losses in these regions.

Hope someone can help.

Bedfiles WholeGenome Compare BioPython • 882 views
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the answer is bedtools

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Bedtools can be found here.

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5.3 years ago

You could use bedmap to count overlapping elements, e.g. to count the number of elements in B that overlap regions in A:

$ bedmap --echo --count A.bed B.bed > answer.bed

Full documentation is available here: http://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html

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