Mapping -> Differential Expression Analysis

This is a demo pipeline. It first uses Bowtie to perform mapping; then calculates the counts of reads based on a reference; finally uses DEGseq to identify differentially expressed genes.

Ka/Ks Calculation

This is another demo that performs Ka/Ks caculation using the Ka/Ks Calculator developed by our lab.

Tool: The Simplest "Pipeline"

Qomo allows you to build pipelines based on various basic tools (modules). All the tools are shown in the left panel of the Workspace tab. To use any one of them, just click on its title. Then a box representing the tool will show in the middle panel of the page. The box is basically a form containing the parameters you need to specify for running the tool. Also notice the question mark (?) on the right of the title of each tool. If you click on it, the usage and relevant information about the tool will pop up. After specifying the necessary parameters, you can click on the RUN button at the top-right corner. Then the pipeline will be submitted as a new job to the server. You can monitor the status of the job on the right panel. After the job is finished, you can check its output on the Data tab.

Here is an example performing differential expression analysis:

Your First Real Pipeline

Now it's time to build a real pipeline.

Save Your Work and Share It with Others

After finishing building your first pipeline, you may want to save it for further use or even sharing with others. Saving a pipeline is easy. Just click on the SAVE button on the top-right corner in the Workspace tab. Type in the title for your pipeline (e.g. "Differential Expression Analysis"). Then type in some description about it (e.g. "Use DEGseq for differential expression analysis, and filter results based on p-values."). Finally, click on Save. You can check all the saved pipelines in the Pipelines tab. (If it is not shown, you may try to refresh the page by pressing "F5" on your keyboard.)

Import Pipelines

You can import pipelines from the Private pipelines or Public pipelines panel under the Pipelines tab. If you load a pipeline, it will override the current pipeline in your workspace. If your merge a pipeline, its components will be added into your current pipeline.