Question: Subscription between genomic regions
0
gravatar for niutster
16 months ago by
niutster80
niutster80 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 • 491 views
ADD COMMENTlink modified 16 months ago by Alex Reynolds25k • written 16 months ago by niutster80
1
gravatar for Alex Reynolds
16 months ago by
Alex Reynolds25k
Seattle, WA USA
Alex Reynolds25k 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 16 months ago • written 16 months ago by Alex Reynolds25k

Thanks, does it install on windows?

ADD REPLYlink modified 16 months ago • written 16 months ago by niutster80

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 16 months ago by WouterDeCoster32k

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 16 months ago • written 16 months ago by Alex Reynolds25k
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