New Cytoband Image Enabled for Assembly Hubs

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Brian Lee

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Feb 7, 2017, 7:07:02 PM2/7/17

to UCSC Genome Browser project announcements

Dear Assembly Hub Developers,

Have you ever wanted to add a chromosome or scaffold view to your assembly hub?

Now you can enable your assembly hubs to include a cytoband image of the scaffold or chromosome you are currently viewing, where the region you are zoomed-in upon will be highlighted to easily show the context of your specific viewing region in the overall chromosome. The cytoband ideogram also allows for more easy navigation, where selecting regions from the image allows you to jump from one end of a scaffold to the other.

If you have cytogenetic band information for your assembly, you can also annotate this information as well to display for each chromosome, including noting a centromere's location. By dividing the chromosome into regions and giving each section a giesma stain reference (gneg, gpos25, gpos50, gpos75, gpos100, acen, gvar, stalk) the overall image will reflect the designated darker or lighter bands.

Find more information here: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Cytoband_Track

To seen a simple example on a plant assembly hub click here::

http://genome.ucsc.edu/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt