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)

Figure 1. Select tasks to include then provide a name and description for the new pipeline

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).

Figure 2. Created pipelines will appear in the Pipelines section of the task menu

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 Pipelines for more information.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.