Saving and running a pipeline
By following the steps in this tutorial, you have built a pipeline. You can save this pipeline for future use.
Select Create new pipeline near the bottom left-hand side of the Analyses tab
Select the Pre-alignment QA/QC, Trim bases, STAR, Post-alignment QA/QC, Quantify to annotation model, Filter features, Normalize counts, PCA, and DESeq2 task nodes to include them in the pipeline. Note that skipping tasks within a pipeline is not allowed if the task uses the upstream output
Name the pipeline as RNA-Seq basic analysis
Give a description for the pipeline; we have noted trimming, alignment, filter genes, normalization, DESeq2
Click Create pipeline (Figure 1)
To access this pipeline in the future, select an unaligned reads data node and choose Pipelines from the task menu. Available saved pipelines will be available to choose from the Pipelines section of the task menu (Figure 2).
After selecting the pipeline, you will be prompted to choose the reference genome for alignment, the annotation for quantification, and the comparisons for DESeq2. After selecting these options, the pipeline will automatically run. See for more information.
Additional Assistance
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