Create Chromosome Wide Distribution Map
Hi all,
I have 185 genes (gene symbols) and corresponding affymetrix ids..I want to create chromosome wide distribution map ..Using R/Bioconductor..or any other tool..
Can anybody let me know how to do it?
Thanks in advance
Nitin
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Eric Fournier
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Nitin
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Nitin
2 answers
Take a look at the ggbio, ideogram, and geneplotter Bioconductor packages. For a non-bioconductor approach, have a look at Circos.
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Sean Davis
You can try the UCSC's hgGenome tool to generate chromosomal mappings for certain model organisms.
In your case, assuming you are working on the human genome:
- Use the Tables tool to create a custom track based on UCSC Genes, but filtered to only contain your specific gene IDs
- Import your custom track in the hgGenome tool.
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More details required. What exactly is a chromosome wide distribution map? You just want to plot their chromosomal locations?
yes i want map all 185 genes on to chromosome map which would show where particular gene is located on chromosome.