Genetic Distribution Of Snp Along Chromosomes - How To Get A Graphical Output?

Question

[Bioch'Ti]

Hi,

I would like to find an "easy" way to get a graphical representation of a set of SNP markers along chromosomes? (I have their names, chromosome number they belong to and their position, in bp, on the chromosome) Is there any dedicated R package(s) or software I can use to produce such figure? I was unable to find what I'm looking for...

Thanks very much, Cheers, Christopher

[Fucitol]

I'm also interested in knowing how to do something similar. I'd like to be able to create a set of chromosomes (using arbitrary lengths (non human organism)) and visualize a set of markers on them given their position.

[Khader Shameer]

Have you tried LocusZoom, snp.plotter or SNAP? See this discussion.

Answer 1

[Mary]

You might look at Genome Graphs tool from UCSC: http://genome.ucsc.edu/cgi-bin/hgGenome

They don't have any sample images, but we did a post on it once way back--it's not a great example but you can get a sense of what it would do if there was data available: http://blog.openhelix.eu/?p=670

They used to have sample data sets to look at but had to retract them in the privacy controversy over the public GWAS data.

Answer 2

[Yogesh Pandit]

This might give you some pointers on how to go about it

Plotting Genome-Wide Association Results