RNAseq Prebuilt Pipeline

How to utilize BioBox prebuilt pipelines to run workflows

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The RNAseq Pipeline connects the STAR and DESeq2 workflows to a user specified number of files, this enables you to quickly launch a pipeline as an alternative to using the pipeline design studio if you have a large number of files. 

  1. Create a project and an Analysis  within your project and select "Pipelines"
  2. Under the design tab select the "RNAseq Pipeline (STAR + DESeq2)" 
  3. Select your read specificity, reference genome, and number of samples you are working with. E.g if you carried out a sequencing experiment with 3 control and 3 experimental samples this number would be 6. 
  4. Select the files you would like to work with from your BioBox library. Selecting "Advanced params" will allow you to customize the parameters associated with the STAR workflow.
  5. Specify which files correspond to the experimental and reference cohorts and launch your pipeline for DESeq2. 
  6. Launch your pipeline. The pipeline with all of your configurations will be saved to your library under pipeline drafts and will be available for you to rerun.