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?
1 answer
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.
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
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.
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