> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/partek/partek-flow/tutorials/bulk-rna-seq/saving-and-running-a-pipeline.md).

# 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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8b9be226df4db35f8facebd328aa5b7be689798e%2Fbulk%20seq%20tut%20create%20a%20pipeline.png?alt=media)

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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-2b372583c1d806cd171142c3075d8664795628ac%2Fcreated-pipelines-will-appear-in-the-pipelines-section-of-the-task-menu.png?alt=media)

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](/partek/partek-flow/user-manual/pipelines.md) for more information.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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