If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
To remove ideograms from the image, the "chromosomes" and "chromosomes_display_default" configuration parameters are used.
If this is set, then any ideograms not explicitly excluded will be drawn. Setting this flag is useful if you want to exclude a few ideograms, but draw the majority of others.
This field is used identify which ideograms to draw and/or exclude. When referring to ideograms, always use the ID of the ideogram as defined in the karyotype file (not the ideogram's text label).
chromosomes = hs1;hs2;hs3
will draw only the ideograms listed. To exclude an ideogram, preceed the ID with "-". Thus, to draw all ideograms but exclude those drawn above
chromosomes = -hs1;-hs2;-hs3 chromosomes_display_default = yes
The order in which the ideogram IDs appear in the "chromosomes" parameter does not influence the order in which they are drawn. To apply a different order, use chromosomes_order, discussed in another tutorial. Without specifying the order, the ideograms are drawn in the order of appearance in the karyotype file.