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Expected learning outcome

To understand the basics of Foundry, and do RNA-Seq analysis with sample mouse data.

Class Materials

You can follow the class materials below.

Session 2:

Before you start

Please go to https://viafoundry.umassmed.edu/ and login into your account. If you have a login issue, please let us know about it (BiocoreStaff@umassmed.edu). We will set up an account for you.

Creating a Run

Once logged in, click on the Projects section at the top menu and click the Add a New Project button. Enter your project name and click OK. This is the place to configure your project. To access pipelines, click the Pipelines tab and then click the Add Pipeline button.

  1. Click on the Add button on "RNA-Seq Pipeline" and close the window.

  1. Now click the Run button of the pipeline on the table.

  1. Run page will be loaded. Under Run Environment, select "New UMASS SCI Cluster"
  2. Enter your work directory in cluster. (e.g. /home/{your_cluster_username}/foundry/)
  3. Under User Inputs, next to reads, click Enter File
  4. Click the Add File button to enter new files.
  5. Next to "1. File Location", enter:
/share/data/umw_biocore/genome_data/mousetest/mm10/gz
  1. and click the magnifying glass button. The box below should populate with files like so:

  1. Next to 3. Collection Type, choose Paired List
  2. Under 4. File Pattern, next to Forward Pattern, type .1. Similarly, type .2 for Reverse Pattern.

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

  1. Next to 5. Collection Name, type rna-seq mousetest paired and Click Save Files
  2. On the "Select/Add Input File" screen which should now have 6 entries, click "Save".
  3. For "mate", choose "pair"
  4. For genome_build, choose "mousetest"
  5. Leave the rest as defaults. Here run_FastQC, run_RSEM, and run_STAR inputs are enabled by default.
  6. Click Run in the top right. RNA-Seq pipeline runs typically take several minutes to complete for this dataset.
  7. Navigate to the Log tab and click on log.txt to see progress on your run.
  8. Once the blue "Running" in the top right changes to a green "Completed" go to the Report tab to see the final reports.
  9. Click on MulitiQC, and scroll to find this plot, which shows aligned reads per library:

  1. Click on Summary to check mapping rates:

  1. Click on RSEM Summary to download the count table:

  1. Click on DEBrowser to do QC and Differential Expression Analysis.

Congratulations! You have run and tested an RNA-Seq pipeline on Foundry!