Question: Subscription between genomic regions
0
gravatar for niutster
13 months ago by
niutster60
niutster60 wrote:

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? Is there any tools?

subscription tools genome • 426 views
ADD COMMENTlink modified 13 months ago by Alex Reynolds24k • written 13 months ago by niutster60
1
gravatar for Alex Reynolds
13 months ago by
Alex Reynolds24k
Seattle, WA USA
Alex Reynolds24k wrote:

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.

ADD COMMENTlink modified 13 months ago • written 13 months ago by Alex Reynolds24k

Thanks, does it install on windows?

ADD REPLYlink modified 13 months ago • written 13 months ago by niutster60

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
ADD REPLYlink written 13 months ago by WouterDeCoster29k

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.

ADD REPLYlink modified 13 months ago • written 13 months ago by Alex Reynolds24k
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