How to utilize BioBox prebuilt pipelines to run workflows
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.
- Create a project and an Analysis within your project and select "Pipelines"
- Under the design tab select the "RNAseq Pipeline (STAR + DESeq2)"
- 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.
- 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.
- Specify which files correspond to the experimental and reference cohorts and launch your pipeline for DESeq2.
- 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.