Frequently Asked Questions:

• Why is the color in the preview image different than the color I've selected for my annotation?
• Why doesn't the color of my annotation match the legend in the preview?
• Why are the colors in my eps image incorrect in Photoshop?
• My annotation file loaded OK, but why can't I see my overlay annotation?
• Why won't my annotation file load?
• What does the list of warnings below the preview window mean?
• Are there any known problems with this service?
• Is there an API I can use?
• Why is the top part of chimp chromosome 2B red?
• Why do some sequence representations have centromeres and others do not?

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?

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.

• GDP currently requires that the seqid column (column 1) use RefSeq accession identifiers, e.g. NC_000001.11. Chromosome identifiers, e.g. chr1, will not be recognized and will show an error.
• GDP does not currently support the upload of GFF3 files that describe alignments using the term "match" (SO:0000343) in column 3. We suggest replacing this term with one that describes the aligned feature (e.g. "gene"), so the data is treated as a feature annotation, rather than an alignment.
• 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 or uploading a supported file type, 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. Common causes of warnings include:

• selecting the wrong assembly (i.e. providing NCBI36 annotations and selecting GRCh37 as the assembly)
• including non-chromosomal sequences (i.e. unlocalized/unplaced/alternate loci/patch scaffolds) in your uploaded file

Are there any known problems with this service?

There are a couple of known bugs parsing uploaded files. The HGVS parser has trouble with some expressions. Please use the 'Support Center' link at the bottom of the page to report expressions that fail. Additionally, files that contain data on non-chromosomal sequences (e.g.  'chr*_random') will be processed, but generate warnings that may be difficult to interpret because the warnings do not refer explicitly to the non-chromosomal sequences.

The "Advanced Formatting" option currently only works with the value in the "ID" field in col 9 of GFF3 files, though you can select multiple rules associated with this field.

Is there an API I can use?

Currently, there is no API. If this is important to you, let us know by using the 'Support Center' 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.

Last updated: 2017-03-09T10:53:49-05:00