The data for this tutorial comes from Fu et al. The file used here was generated from limma-voom but you could use a file from any RNA-seq differential expression tool, such as edgeR or DESeq2, as long as it has the required columns (see below). To generate this file yourself, see the RNA-seq counts to genes tutorial. To generate a volcano plot of RNA-seq results, we need a file of differentially expressed results which is provided for you here. In a volcano plot, the most upregulated genes are towards the right, the most downregulated genes are towards the left, and the most statistically significant genes are towards the top. These may be the most biologically significant genes. It enables quick visual identification of genes with large fold changes that are also statistically significant. A volcano plot is a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change). The Workbench is now ready to use.Volcano plots are commonly used to display the results of RNA-seq or other omics experiments. You can now close the Workbench and then start it up again as a standard user. Launch the plugin manager and install any plugins you downloaded earlier by clicking on the Install from File button. If it does not, then you can launch it yourself by choosing the menu option:ġ0. The License Manager of the Workbench should start up automatically when you start up the Workbench. To locate an existing license file from a Workbench installed to a different area of the machine, look in the folder called licenses for that other installed Workbench copy. If you have downloaded a license file (step 3) or you have chosen to install a minor update to a new location on your machine rather than the existing installation location, then install the license file by choosing the option Import a license from a File within the License Manager. Once the software is installed, start up the Workbench as an administrative user.ĩ. Run the Workbench installer as an administrative user on the non-networked machine.Ĩ. This would usually be done by saving to an area accessible to that machine, or by saving the files to a USB stick or other form of portable storage available to you and loading them onto a non-networked machine.ħ. Transfer the Workbench installer, plugin files, and the license file to the non-networked machine you wish to install the software on. If you are upgrading the Workbench with another version in the same release line, then you do not need to download a license file. As an example, v20.0.x and 20.0.4 are in the same major release line, as both have "20" as the first digit, and they can be run using an existing license file that supports the 20.x line.Ħ. That information is written for the QIAGEN CLC Genomics Workbench but is relevant for other CLC Workbenches also. Information about how to accomplish this can be found at:ĥ. 12.x -> 20.x), then you will need to download a license file for the (non-networked) machine you plan to install the Workbench on. You will need your license order ID and the host ID of the machine the software will be run on for this. If you are installing this software for the first time or are upgrading to a new major version (e.g. The relevant plugin files can be downloaded by clicking the button in the Download column on that page.Ĥ. If you wish to install any of the available Workbench plugins, please download the Workbench plugin files from the plugin page. How do I install or upgrade my Workbench on a non-networked machine?ĬLC Workbench software can be installed on a machine that is not connected to the external network by doing the following:ġ. Using a machine that is connected to the internet, download the installer file for the CLC Workbench.Ģ. Information about how to download the installer file for your Workbench can be found in the related FAQ: Where can I get installer files for QIAGEN CLC software?ģ.
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