Question: Genetic Distribution Of Snp Along Chromosomes - How To Get A Graphical Output?
6
gravatar for Bioch'Ti
8.6 years ago by
Bioch'Ti1.0k
France (Avignon)
Bioch'Ti1.0k wrote:

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

visualization snp chromosome • 4.9k views
ADD COMMENTlink modified 8.5 years ago by Yogesh Pandit500 • written 8.6 years ago by Bioch'Ti1.0k

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.

ADD REPLYlink written 8.6 years ago by Fucitol140

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

ADD REPLYlink modified 12 weeks ago by RamRS25k • written 8.5 years ago by Khader Shameer18k
5
gravatar for Mary
8.6 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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.

ADD COMMENTlink modified 5 months ago by RamRS25k • written 8.6 years ago by Mary11k
1
gravatar for Yogesh Pandit
8.6 years ago by
Yogesh Pandit500
United States
Yogesh Pandit500 wrote:

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

Plotting Genome-Wide Association Results

ADD COMMENTlink written 8.6 years ago by Yogesh Pandit500
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