Accessing results

Using Workflow Invocations

For accessing the results from the Primary analysis workflow, one can access all the information regarding the workflow under Workflow Invocations. Under User > Workflow Invocations, all the workflows that have been run by you should appear. When you expand the workflow invocation that you are interested in, you can look at

  • The inputs (all the files you provided),

  • all the outputs (all the outputs that were generated by tools in the workflow),

  • output collections (folder of output files from a tool), and

  • all the steps of the workflow.

One can use the expand button for each of them and look at the file under each of them. For each tool, one can either view the result file, edit the filename or delete the file. For each tool, expanding the result file will reveal the details of the run. If you would like to see the contents of the file itself (in the case of text files, log files, or pdf files with plots), the view (eye icon) next to the result file will help view your result file. However, if it’s an HTML file, expand the tool output, go to the three buttons, and click on Download and you can view the downloaded HTML file in your browser.

Using Histories

When you started working on the Primary Analysis workflow, you started by sending results to a new history, naming it with an intuitive name, and then running the workflow. All your results should be available under that history. You can access that particular history by going to User > Histories. This will show you all the histories that you have created. This should display the history that you are interested in. You can access it by clicking on that history and it will display it on the right side of the page. You can scroll through the history and choose the tools and the result files that are generated by each of them. You can access and examine them in the same as you would in the case of accessing it through the workflow invocations.

Looking at individual results

DESeq2 -

If you would like to access the plots and normalized counts from DESeq2, use the eye icon for “DESeq2 plots on data N” and “Normalized counts file on data N” to access them.

Gene ontology -

If you would like to access the plots and categories from GO, use the eye icon for “go plot”, “go_overrepresnted”, “go_underrepresented” to access them.

KEGG -

If you would like to access the plots and categories from KEGG, use the eye icon for “KEGG pathways”, “KEGG genes” to access them.

Heatmap -

If you would like to access the heatmap plot, use the eye icon for “heatmaps” to access them.