Question: Map Cnv?
0
gravatar for bioinformatics123
8.5 years ago by
bioinformatics12310 wrote:

If we have list of cnvs and their start stops and another list of genes and their start and stops..How can we map CNV region i.e its start and stop to a gene and find if there is an overlap(whether gene falls outside this region or within this region) in an automated way?

genomics • 1.9k views
ADD COMMENTlink written 8.5 years ago by bioinformatics12310
2
gravatar for seidel
8.5 years ago by
seidel7.1k
United States
seidel7.1k wrote:

It may depend on what you mean by automated, but this is a fairly simple programming task. It would make a good exercise for someone trying to learn a scripting language and they could probably figure it out in an afternoon. There are many methods for doing this in R (see this recent question). For someone who doesn't want to learn any programming, you could do this with Galaxy. It can also be done fairly easily in excel.

ADD COMMENTlink written 8.5 years ago by seidel7.1k
2
gravatar for Pierre Lindenbaum
8.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

Use betools intersectBed : http://code.google.com/p/bedtools/wiki/Usage#intersectBed

ADD COMMENTlink written 8.5 years ago by Pierre Lindenbaum131k
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