Subscription between genomic regions

Question

[niutster]

Hi,

I have two files contain genomic regions, each row of file contains chromosome name, start site and end site. Each row determines a genomic region, I am interested to count how many regions are shared between these files. I don't want to determine regions are completely the same. How can I identify them? Are there any tools?

Answer 1

[Alex Reynolds]

You can use BEDOPS bedmap --count to count the number of overlaps between reference and map files:

$ bedmap --echo --count --delim '\t' fileA.bed fileB.bed > answer.bed

The default overlap criterion is a minimum of one base of overlap. You can adjust this to be more stringent, if need be. See bedmap --help or the online documentation for more detail.

[niutster]

Thanks, does it install on windows?

[WouterDeCoster]

If that is a requirement then:

• You should mention that at the beginning of your post
• You should realise that many tools are unavailable for you

[Alex Reynolds]

It installs in Cygwin under Windows, or you can run Linux inside VirtualBox under Windows, and use this kit within a Linux environment. It does not run directly under Windows, however, and not many bioinformatics tools do.