Question: Graph of BED data on Chromosomes
2
gravatar for mujupas
5.1 years ago by
mujupas50
Japan
mujupas50 wrote:

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!

chromosome graph density plot bed • 4.5k views
ADD COMMENTlink modified 2.7 years ago by prakashgenetics0 • written 5.1 years ago by mujupas50

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!!

ADD REPLYlink written 2.7 years ago by prakashgenetics0
5
gravatar for Alex Reynolds
5.1 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

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.

enter image description here

ADD COMMENTlink modified 2.7 years ago • written 5.1 years ago by Alex Reynolds29k

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

Nice Alex!

ADD REPLYlink written 5.1 years ago by Jonathan Crowther180
1
gravatar for Jonathan Crowther
5.1 years ago by
Leuven/Dublin
Jonathan Crowther180 wrote:

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

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Jonathan Crowther180
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