Step 1: Select Genome Information
Set up your ideogram by selecting an organism and a representation. Representation options are:
Cytogenetic
Sequence 
As soon as you select an organism, a preview will be made available. To see how additional selections affect the figure, hit the 'Refresh' button at the top of the 'Ideogram Preview' window.
To request the addition of an organism, write to us.
Step 2: Set-up your layout
- How fonts are rendered: the font, size and colors can be selected.
- The layout of the chromosomes (horizontal or vertical).
- The chromosome alignments (Top, bottom or centromere aligned).
- The number of rows in the figure (1 or 2).
- The size of the chromosomes and whether band labels should be included.
- Limit the number of chromosomes shown.
Step 3: Upload your Annotations
Upload your annotation file(s) and format your annotations. You can load up to 16 annotation tracks to be displayed next to the chromosome and 1 annotation track that can be used to produce an 'overlay'. Annotation can be provided using basepair coordinates or cytogentic coordinates (see the help page for more details).
If your annotations are in sequence coordinates, upload a file that is formated in one of the following formats:
If your annotations are in cytogenetic coordinates you can just upload a list of the cytogenetic locations; for example:
1q21
1q21-q22
If you use a GFF style annotation file, you can use the 'Advanced formatting' option to render specified features in the file differently (see the help page for more details).
Step 4: Download your Figure
Once you have things displayed the way you would like you can download your figure in several formats, including those suitable for editing in a graphics program for submission to a journal.
next to file.