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
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Color:
warning Ideogram Preview
Download format:
.png

What is the Genome Decoration Page?

The Genome Decoration Page (GDP) is a service that allows users to upload their own annotation data and create a figure showing that annotation distributed on the genome. Annotation can be shown as a track, or set of tracks, drawn next to the chromosome. One annotation track can be selected to be drawn as an 'Overlay', such that the annotation information is drawn on top of the chromosome representation. 

How does this work?

Step 1: Select Genome Information
  • Select an organism from the pulldown menu. Currently we support mammalian genomes that have a chromosome level assembly. If you would like to have an organism add, please use the 'Write to Help Desk' link at the bottom of the page to make your request. As soon as you select an organism, a preview will be shown. To see how additional selections affect the figure, hit the 'Refresh' button at the top of the 'Ideogram Preview' window.
  • Select the genome representation you would like. This involves selecting an assembly and a representation. Choosing 'cytogenetic' means the chromosomes will be rendered with standard banding patterns. Choosing 'sequence' means there will be no bands drawn, just a chromosome representation with centromeres (when the data is available). If you choose 'cytogenetic' you can still provide your annotation data in sequence coordinates. Whether you chose 'cytogenetic' or 'sequence' you will still need to select a specific assembly as the cytogenetic to sequence relationship is different in different context.
  • A preview of your images will be shown to the right of the selection menus. As you update the form, select the 'Refresh' button at the top of the image. You can select the 'Refresh' button as often as you would like and you can see how your selections affect the image.
Step 2: Set up your layout
  • Define the layout for the figure:
    • Select the font type you would like used in the figure.
    • Define how you would like the chromosomes aligned
      • Aligned at the top.
      • Aligned at the bottom.
      • Aligned at the centromere.
    • Define whether the chromosomes should be drawn horizontally or vertically.
    • Choose whether the chromosomes should be displayed on a single line or on two lines.
    • You can adjust the size of the chromosomes by typing the size, in pixels, (height and width) by typing the sizes in the text box.
    • Next, define if you would like chromosome labels displayed, and whether they should be displayed before (or on top) or after (or on bottom) of the chromosome.
    • Pick the font size and color for the chromosome labels.
    • If you chose a 'cytogenetic' representation, you can choose whether band labels are displayed and how they are displayed.
    • You can also set up a figure legend if you wish to have one on the page. You can select the position relative to the chromosomes (below or to the right) or select 'None' if you don't want a figure legend. You can also adjust font size and color as well as text direction.
Step 3: Upload your annotations

Annotations can be displayed on the images as a track, that is features drawn beside the chromosome, or as an overlay, that is an image drawn on top of the chromosome representation.

Example of a track annotation: Annotation file: track example Example of an overlay annotation: Annotation file: overlay example

You can only define one file for overlay annotation, but you can add up to 16 files that will be displayed as separate annotation tracks. To add annotations:

  • Upload your annotation file.
    • 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 cytogentic locations; for example:
      1q21
      1q21-q22
  • Choose the color and shape you would like to use for your annotations.
  • Select the width of the annotation track. 
  • Provide a 'Track name' for use in the figure legend. 
  • To add additional tracks, select the 'Add track' button and repeat Annotations steps 1-4.

Note: If the upload function cannot read your file, you will be notified via an alert. If the file is read properly, but there are sequence locations in the file that the process doesn't know how to interpret you will be given a list of warnings below the ideogram preview. These warnings will not show up until you hit the 'Refresh' button. If you have loaded multiple files, the warnings within each file will be listed with a header denoting where the warning list for each file begins. 

We know the HGVS parser has trouble with some expressions. If you have trouble with an HGVS expression, please use the 'Write to Help Desk' link at the bottom of the page and report the expression to us so we can improve our parser.

There is also a known bug parsing some data downloaded from UCSC. If the data contain features on a 'random' chromosome, you will receive no warning about unlocalized sequence in your file. The unlocalized and unplaced sequences won't be rendered on the ideogram, so this will not affect the figure, but you should still recieve information about this.

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.