Frequently Asked Questions:

Why is the color in the preview image different than the color I've selected for my annotation?

Depending on your annotation, if the marks are small, the color can be blended with the color used for the border of the annotation.  When the file is created as .eps or .svg, the colors will be correct.

Why doesn't the color of my annotation match the legend in the preview?

Just like the preview color not matching the annotation color, depending on your annotation, if the marks are small, the color can be blended with the color used for the border of the annotation.  When the file is created as .eps or .svg, the colors will be correct.

Why are the colors in my eps image incorrect in Photoshop?

When opening the eps image in Photoshop, choose File->Open.  Navigate to the downloaded file and open it.  Then in the dialog that appears that says "Rasterize EPS Format" make sure to choose RGB Color for the mode near the bottom of the dialog.

My annotation file loaded OK, but why can't I see my overlay annotation?

There could be two reasons for this. If your annotated objects are very small, the screen may not have sufficient resolution to show these as an overlay. Additionally, if you selected a cytogenetic representation and keep the default black color for the overlay, your overlay annotation may blend into the ideogram representation. Overlay annotations typically look better with a sequence representation.

Why won't my annotation file load?

Your file may not be formatted correctly. Here is the list of currently supported annotation files. If you are trying to upload a Word file or an Excel file, this will fail. Only text files are supported. If you are having trouble generating these files, write to us and we'll try to help you fix the problem. 

What does the list of warnings below the preview window mean?

Importing an annotation file is a complex operation and there can be errors during this process. If the upload process cannot read your file at all, you will receive an error notice immediately via an alert window. In some cases, the data can be read but there may be sequence locations within the file that the process can't interpret. We will do our best to handle the locations we understand (and display them on the ideogram) and provide you with a list of warnings for the locations we can't interpret. A common cause of these warnings is selecting the wrong assembly (i.e. providing NCBI36 annotations and selecting GRCh37 as the assembly). 

Are there any known problems with this service?

There are a couple of known bugs parsing uploaded files. The HGVS parser is in an early stage and will have trouble with some expressions. Please use the 'Write to the Help Desk' link at the bottom of the page to report expressions that fail. Additionally, files that contain data on 'chr*_random' will be processed, but you won't see a warning about the unlocalized sequence that is in your file. As unlocalized sequence can't be rendered on the ideogram this will not affect the figure, but should be reported.

Is there an API I can use?

Currently, there is no API, but we are planning on developing a REST API that will be available with the next release of this service (currently unscheduled). If this is important to you, let us know by using the 'Write to Help Desk' link at the bottom of the page.

Why is the top part of chimp chromosome 2B red?

This is reflective of the data that was submitted to GenBank. Several biological gaps have been introduced at the beginning of chromosome 2B in order to preserve coordinate space in an earlier version of the assembly.

Why do some sequence representations have centromeres and others do not?

Some submitters of assembly data model biological gaps (centromeres, telomeres, etc) when they submit their assembly data to GenBank/EMBL/DDBJ. The chromosome drawings we present here are based on the submitted assembly date.

Write to the Help Desk

Last updated: 2013-05-21T17:01:42-04:00