Graph of BED data on Chromosomes

Question

[mujupas]

Hi!

I have a quick question: I have some BED files (intervals pointing at transposons position) and I want to plot them to show the density on human chromosomes.

Any suggestion?

Thank you in advance!

[prakashgenetics]

Hi everyone, I am trying to plot QTLs from the .BED file downloaded from cattle QTLdb, now i want to plot these qtls on respective chromosomes along with LD blocks which was retrieved from Haploview. I am unable to get it, so please suggest me exact solution for the same.

Thanks in advance!!

Answer 1

[Alex Reynolds]

To visualize, perhaps look into preparing a custom track on the UCSC Genome Browser.

Once you have added your custom track, you can use the Genome Graphs functionality to visualize it on chromosome ideographs (you can also visualize other signals with the same tool) and the View > PDF menu option to export a PDF file.

[Jonathan Crowther]

This method looks great and doesn't require extra coding in R!

Nice Alex!

Answer 2

[Jonathan Crowther]

If you have some experience in R you could plot some nice karyograms with a plot as a line or you can also include the cytoband with a marker above the chromosome. I think they look quite nice and would be useful for you.

Everything you need is here but if you want some additional help just message me :)

http://www.tengfei.name/ggbio/docs/man/layout_karyogram-method.html