You are free to write any personalized notes in the Description box. These notes will be displayed in the Details box when viewing Circos, and can serve as future reference.

You can either have a Homo sapiens or a mouse karyotype.

You also have the option to use the entire karyotype or only some chromosomes. It the latter case, please follow the proper orthograph, as demonstrated:

chr1;chr6;chr9 would display chromosomes 1, 6 and 9

Any changes will cause Circos to fail.

Labels will be displayed on the outter side of your ideogram. Only .txt are accepted and they must be correctly formatted:

#chr 	start		end		value
...
chr1	245385825	245401941	ZNF124

Labels will be displayed as the largest and innermost track of your Circos. You can give a brief name/description to your links. Only .txt are accepted and they must be correctly formatted:

#from	start	end	#to	start	end
...
chr1	400	550	chr3	500	750

When displaying links, it is recommanded to show no more than 4 tracks (including the gene density track). Otherwise, tracks may overlap.

The data used to generate the Gene Density histogram is from the UCSC Genome Browser (500kb). You can add and remove as many tracks as you want. For each one, you must choose a graphical representation (histogram, heat plot, scatter plot or tiles) and upload a .txt file. You can also give each track its own name, which could useful for future reference. Again, the submitted file must be correctly formatted:

#chr	start	end	value
...
chr19	305575	344791	3.11363

It is recommanded to show no more than 5 tracks (including the gene density track). Otherwise, tracks may overlap.

For more information on how to format your data files, please refer to the Circos tutorials.