How to plot an ideogram for two bed files with different number of rows in R?

Question

[mohamad.merhi96]

I'm trying to create an ideogram for human vs mouse to recognise the common and different transcription factor binding sites . I have two bed files representing starts and ends of transcription factor binding sites. My problem is that the human bed file is larger than the mouse one.

I need them to have the same number of rows otherwise RCircos will produce an error saying that the number of rows in the two datasets are different.. "arguments imply differing number of rows"

Any suggestions?

Answer 1

[Alex Reynolds]

Cutting out rows in one subset doesn't really make sense. You need different ideograms for the two species, and show the alignment of chromosomes between species, where there are deletions, insertions, and novel regions unique to the species. You could use UCSC's ideogram graphing tool, or write one with Circos, say, to display chain tracks that display the alignment of genomic intervals for two species (human and mouse). Then plot your species-specific TF binding sites atop each per-species ideogram.

[mohamad.merhi96]

Frankly I don't think approaching the problem using Circos that way is feasible ? I'm not quite sure, I used leftover chains to produce my mouse bed file from my human bed file , wouldn't it be backtracking to use the leftover chains? Additionally I didn't quite get the visual product of the Circos suggestion.