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.
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:
- Click on DEGseq
- Click on the input box labeled Expression. Select "PUBLIC/GeneExpExample5000.txt" in the open file dialogue.
- Click on the input box labeled Score. Type in a name for the output file (e.g. "de").
- Click on RUN. You should see the submitted job on the right panel. After it is finished, click on Data to check the output.
Your First Real Pipeline
Now it's time to build a real pipeline.
- Following previous example, click on Line filter in the toolkit panel. This is a tool for filtering lines. Here we use it to remove genes with a p-value less than 0.05.
- To use the output of DEGseq as the input of Line filter, drag the little green box on the right of the input box labeled Score to the blue box on the right of the input box labeled Input. Now there is an arrow showing the data flow between the two tools.
- Type in "$6 < 0.05" in the input box labeled Expression, because column 6 of the output of DEGseq is the p-value, and "$6" means the value in the 6th column. You can get to know the meaning of the output by reading the usage of the tool. (Hint: click on the question mark (?).)
- Finally, specify a name for the output of Line filter (e.g. "filtered"), and click on RUN. After the job is finished, you can check the output in the Data tab.
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.)
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.