Thursday, March 8, 2012

Scaffold sequence configuration function

The "Contig View" function has officially retired - been replaced by the scaffold sequence configuration function where arbitrary and flexible choice of scaffold sequence can be chosen for display.

At control panel go to "Genomic view" --> "Scaffold sequence" to view the interface:


The table shows list of scaffold sequence currently in use, and their order of appearance on the horizontal axis of genome heatmap.

To add more sequences to the list, click "Add more" button, a new panel will appear:



The sequences have been grouped. In this case of human genome, two groups are shown in the panel, click to reveal list of items:


The "chromosome" group contains fully assembled chromosomes, and the "other" group contains anything else. Sequences are presented as clickable rectangles for you to select. Box filled in blue indicates the sequence is in display, and unfilled means it isn't and can be added.

To remove from display, click X button to mark for removal, the "Update" button will appear. Click button again to unmark. You can mark multiple sequences before clicking the update button to remove them:



If you click the chromosome name, or anywhere except the removal button, the sequence will be in bold face indicating it is selected. Only one item can be selected a time. More buttons will appear allowing you to move this item in the list:


Use arrow buttons to move selected item along the list. Once moved, you need to click "Update" button to take effect. Click the Knight button to show this sequence in its entirety.

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The Bird's eye view has identical scaffold configuration function, available from the Bird's eye view panel (click button Configure and then select "scaffold sequence"):


An identical looking panel will appear:


There you can configure scaffold sequences to be used in Bird's Eye View, which is totally independent from what is used in genomic view.


And that's it. This function replaces the cluttered design of Contig View, and is the first step towards building the Repeat Browser -- where over 1000 repeat subfamilies are available, and user needs to be able to browse and select them in an intelligent manner (following Class > Family > Subfamily hierarchy is essential instead of looking through a huge list).