RCircus error while drawing ideogram
Entering edit mode
5.9 years ago

I have a human bed file that is mapped to a mouse bed file. The thing is, some of the human rows ( regions) map to many regions in the mouse.bed So one row from human.bed file has several rows in mouse.bed file.

I want to draw an ideogram and establish the links between both bed file to see the connections . Since Link in RCircos requires the two bed files have same number of rows, I followed these steps:

-I mapped each row from human1.bed alone, and outputted it to a mouse1.bed alone

-I checked if the human1.bed has less rows than mouse1.bed, in that case it's a one to many mapping . So I duplicated the row in human1.bed in order to match the number of rows in mouse1.bed

-I did this for all files and then merged all mouse1.bed,mouse2.bed,mouse3.bed....etc into mouse.bed . Likewise for human.bed .

However when I try to establish the links in RCircos with the command RCircos.Link.Plot(link.data, track.num, FALSE,lineWidth=10);

I get that some error in RCircos.Validate.Genomic.Data saying that some chromosome in plot data is not in ideogram .

Could it be because of the duplicate rows in human.bed file?

R genome alignment mapping • 1.3k views
Entering edit mode
5.7 years ago
theobroma22 ★ 1.2k

What you tried was quite shrewd of you! However it doesnt work like that. You need to map each row in Human to each row in Mouse, so for multiple links to one row you need to demonstrate this in the file. Like Row H1 Row M1 Link A; Row H1 Row M2 Link A; Row H1 Row M3 Link A...and so on. Your link file should look something like this, so their both the same size. If you still can’t get it paste your code and show me your link file. You can also check my posts as I’ve been successful in helping others with circos!


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