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?