Flow Documentation

Partek Flow Documentation

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  • Select Make a pipeline near the bottom left-hand side of the browser window
  • Select Tim bases, Pre-alignment QA/QC, Align reads, Quantify to annotation model, Post-alignment QA/QC, Normalize counts, PCA PCA, and Gene analysis task nodes to include them in the pipeline
  • Name the pipeline; we have chosen RNA-Seq basic analysis 
  • Give a description for the pipeline; we have noted trim <20, STAR, normalize with total count and add 0.001, GSA 
  • Select Make pipeline (Figure 1)

Numbered figure captions
SubtitleTextSelect tasks to include then provide a name and description for the new pipeline
AnchorNameMaking a pipeline

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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). 

 

Numbered figure captions
SubtitleTextCreated pipelines will appear in the Pipelines section of the task menu
AnchorNameRunning a pipeline

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After selecting the pipeline, you will be prompted to choose the reference genome for alignment, the annotation for quantification, and the contrasts for GSA. After selecting these options, the pipeline will automatically run.

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