This function allows viewing data on unassembled contigs instead of assembled chromosomes. At control panel, go to "Genomic view" → "Contig view", the Contig View panel will be shown:
A number on the right side of panel banner tells how many contigs this genome assembly carries. So this function doesn't apply to genomes without unassembled contigs (like mouse mm9). In such cases, the contig panel will be hidden:
As indicated, there are two ways to determine which contigs you would like to see. At the "Way 1" panel, directly enter contig names and press "Add", contigs passed validation will be placed in the "List for display" box:
The other way lets you select contigs purposefully by their values of three metrics: length, number of genes, and GC content. At "Way 2" panel, you can find three images on which you drag and select. Click the "help" button to show the tip:
Once selected, the contigs will be placed in the "Select for list" box. Following is the selection of gene-rich contigs. If you re-select for another time, contents in this box will be refreshed:
From here you will decide which contigs to put in "List for display" box. You can click on the ✔ button of a contig, or press "Add'em all" button to select all of them.
And finally at "List for display" box, press "Display" button to run Contig View:
The genomic feature track is gene body. It shows that these contigs do carry a lot of genes, but none of the heatmap tracks have any signal at these regions, due to the fact that people usually exclude contigs in read-alignment.
Finally, click the "turn off" button to switch off Contig View and go back to genome view.
Last modifed: 09/28/2011