Expected learning outcome

To understand the basics of running a pipeline in Foundry by running the TE Transcripts analysis pipeline on sample mouse data.

Before you start

Please go to https://www.viafoundry.com and login into your account. If you have any issues logging in, please let us know (support@viascientific.com) and we will help to create an account for you.

Creating a Project

In Foundry, analysis is organized by project. Each run belongs to a project and a project can consist of multiple runs.

Once logged in, to create and configure a new project click on the Projects tab in the top menu and select Add a New Project button in the dropdown. In the pop-up, give the project a name (e.g. TE Transcripts Tutorial) and click save.

Attaching Pipeline to Project

To help with organization, pipelines used in a project are attached to that project.

Note: The same pipeline can be attached to multiple projects.

To attach a pipeline select the Pipelines tab and then click the Add Pipeline button.

Locate TE Transcripts, click on the Add button, and then close the window.

Creating a Run

Once the project is created and a pipeline is attached, you are ready to create a run:

1. Click the Run button next to the TE Transcripts entry in the table to load the "Run Page"

   

2. On the run page, under "Run Environment" select viafoundry

3. In the Inputs section, next to FASTQ Input, click Enter File
4. In the files tab, click Add File button to enter new files.

5. Next to "1. File Location", enter:

   gs://via-scientific-nprd-bucket/viafoundry/run_data/test_data/fastq_mouse
   

6. Click the magnifying glass icon. The box below will populate with files like so:

   

7. In the 3. Collection Type dropdown, select Paired List

8. Under 4. File Pattern, next to Forward Pattern, enter .1. Similarly, enter .2 for Reverse Pattern.

   

9. Click Add All Files button. You should now see 6 entries below.

   

10. Next to 5. Collection Name, enter mousetest paired. The final three boxes can be left blank. Click Save Files

11. The "Select/Add Input File" screen will now have 6 entries. Click "Save".
12. For "Library Type", select pair
13. For "Genome Build", select mouse
14. For "Groups file", click Enter File

15. In the "File Location", enter:

    gs://via-scientific-nprd-bucket/viafoundry/run_data/test_data/fastq_mouse_metadata/groups.tsv
    

16. Click Save

17. For "Comparison file", click Enter File

18. In the "File Location", enter:

    gs://via-scientific-nprd-bucket/viafoundry/run_data/test_data/fastq_mouse_metadata/comparisons.tsv
    

19. Click Save

20. Leave the rest of the inputs as defaults
21. Click Run in the top right and then select Start. For this dataset, the TE Transcripts pipeline run typically takes several minutes to complete.
22. Navigate to the Log tab and click on log.txt to follow the progress of your run.
23. Once the status bar in the top right changes from a blue "Running" status to a green "Completed" status go to the Report tab to see the final reports.

24. Click on Deseq2 to open the "Differential Expression" section. Select the first file on the left tab (exper_vs_control_DE.html). This is a differential expression report for the comparison. The report can be expanded to fit the full screen with the button on the top left.

    

25. Launch the GSEA Explorer application by clicking the second file on the left tab (exper_vs_control_DE.Rmd) and then click Launch

Note: For the purposes of speeding up the runtime of this tutorial, the demo dataset has been downsampled to only include a few genes. Differential expression analysis graphs and Gene Set Enrichment Analysis graphs will look very sparse with this dataset.

Congratulations! You have run and tested the TE Transcripts pipeline on Foundry!