Gene Read Depth Tool

A tool to visualize the read depths of specified genes, mapping the sequenced genomes of 40 wild isolates of C. elegans from the Million Mutation Project back to the reference N2 genome.

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Show results from isolates:

Formatting options:

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Select Colour

Apply Colour To:

Enter the gene names below

How to use GDepth

Selecting genes

This tool works off of either the common name of some gene (such as cyp-13A1), or the WormBase sequence name (such as T10B9.8). If you have a list of genes of interest in either format enter them into the 'Exact names' box, separated by commas, spaces, or newlines.

If you would like to view results for an entire gene family, enter the common name of one or more families into the 'Gene families' box. As an example, to view the cytochrome P450 genes, enter 'cyp, daf-9'. This will match to all of the named cyp genes, plus the single differently named gene daf-9. If you wanted to view only the cyp-13A genes, you could exclude all of the others by instead only entering 'cyp-13a'. If you enter 'gst' into the 'Gene families' box, you will notice that it also returns results for the gstk and gsto genes. You could exclude these from the graph by entering 'gstk gsto' into the 'Exclude gene families' box, or by simply using 'gst-' in the 'Gene families' box.

Features of the graph

The returned graph shows the average read depth for each gene, where each data point indicates the average read depth for 1 C. elegans isolate. Holding your mouse over a point will highlight all other points from that same isolate, and will identify that point in the top box. All 40 isolates are identified above the graph, and the checkboxes can be used to show or hide them as desired.

Clicking on a gene name, either on the x-axis or in the top information box, will open the relevent entry from WormBase. Mouseing (sp) over a gene name also provides the option to remove that gene from the graph, or to open that region of the genome using CDepth (COMING SOON™).

You can draw a selection on the graph using your mouse, and the top information box will display how many points are contained within. Clicking on that number in the info box will open a new display showing which isolates and which genes were selected (COMING SOON™).

To do list

  • Add button to save graph as an image.
  • Add a slider to zoom in Y range.
  • From click selection, click on number to provide more information.
  • Implement the various formating options for the graph.
  • Add the option to to set each strain as a different colour.
  • Add ability to remove a gene from graph, by mouseover gene name.
  • Add ability to mouseover gene name, and click to open that genomic region with CDepth.
  • Add basic outlier detection.