This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Compare a long list of BEDFiles against a whole genome/ chromosome ?

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.

whole-genome biopython bed
• 1,600 views • link
updated by Ram Ram • written by dearbbhyc • dearbbhyc

Bedtools can be found here.

• 1 views • link
written by GenoMax GenoMax

1 answer

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

• 1 views • link
written by Alex Reynolds Alex Reynolds

Log in to answer this question.

More posts like this