Question: Identifying CpG islands given a vcf variant file
0
gravatar for sagi.polani
5.2 years ago by
sagi.polani80
Israel
sagi.polani80 wrote:

Hi all,

 

I 'm looking to find a way to identify CpG islands around a given set of variants listed in a vcf file. Any ideas?

 

Thanks!

 

Sagi

cpg islands vcf • 1.9k views
ADD COMMENTlink modified 4.6 years ago • written 5.2 years ago by sagi.polani80
3
gravatar for Devon Ryan
5.2 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:
  1. Download a BED file of CpG islands from UCSC.
  2. Use bedtools closest to find the nearest CpG island.

You could also use GenomicFeatures in R.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Devon Ryan95k

Is this relevant also for non-human data?

ADD REPLYlink written 5.2 years ago by sagi.polani80

It's for any species with CpG islands available from UCSC. If there are no such annotation tracks for your organism, you'll need to generate them.

ADD REPLYlink written 5.2 years ago by Devon Ryan95k

OK, so now I know that such a track does not exist for my organism. How do I continue from here?

ADD REPLYlink written 5.2 years ago by sagi.polani80
1

Have a look at this package from Rafael Irizarry's group.

ADD REPLYlink written 5.2 years ago by Devon Ryan95k
0
gravatar for sagi.polani
4.6 years ago by
sagi.polani80
Israel
sagi.polani80 wrote:

Thanks Ryan!

ADD COMMENTlink written 4.6 years ago by sagi.polani80
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