Map Cnv?

Question

[bioinformatics123]

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?

Answer 1

[seidel]

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.

Answer 2

[Pierre Lindenbaum]

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