Genome Information

Organism:
Representation:
Chromosomes:

Layout

Font:

Ideogram: Vertical

Alignment:
Orientation:
Number of rows:
Chromosome size (px):
Chromosome labels:
Font size: Text color:

Band labels: None

Orientation:
Settings:
Font size:
Alignment:
Text color:

Legends: None

Position:
Text:
Columns:
px
Font size:
Text color:

Annotations

delete track
Color: Shape: Advanced formatting
Color: Shape: % Advanced formatting
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Enter the location(s) you want highlighted as a cytogenetic location (5p15) or a sequence location (e.g. chr1:start-stop)
Highlight legend
Reset All
Color:
warning Ideogram Preview
Download format:
.png

Step 1: Select Genome Information

Set up your ideogram by selecting an organism and a representation. Representation options are: 

Cytogenetic Example of a cytogenetic representation Sequence Example of sequence representation

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

Select the layout you would like. You can select:
  • 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. 

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. 

Color Picker

Red
slider
Green
slider
Blue
slider
Hue
slider
Saturation
slider
Brightness
slider

Specify format for annotations with a specific value

Track:Track name
Defaults
Shape: Color: %
Specify formats using column:
Value-shape format rules
remove binding
Shape:
Value: -
You can re-upload the file by clicking the re-upload icon reload next to file.