Mapping of gene

Question

[rakeshmbb]

Hello everybody...I have co-ordinate of nearly 200 genes. I want to make a map using the co-ordinate. can anyone tell me how can I do that. Thanks in advance

[andrew.j.skelton73]

A map of what?

[bioguy24]

Are you trying to map genes to coordinates?

[rakeshmbb]

Hi cmccabe.....I have coordinate of genes like below.

Chromosome 1
Gene1 4563246
Gene2 67453541
Gene3 67843736
gene4 546354387
..........................

Now I want to make a simple chromosome map to visualize these genes position.

Answer 1

[andrew.j.skelton73]

Check out this. The first few slides show how to make an ideogram, and they return ggplot2 objects (or that's extractable from a slot of the returned object). Because they return ggplot2 objects, for the relevant chromosome, you can mark the start sites you've got by using a vertical line.

Answer 2

[kozhaki.seq]

You can use GenomePixelizer to map your genomes to chromosome. Unlike Circos, the tool generate linear chromosome image and the best thing is 'tool generates HTML codes which can be used for making clickable image on embedding some webpages.