Partek Flow Documentation

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This guide gives the basics of Partek® Flow® usage. Partek Flow can be installed in either a server, computer cluster or on the cloud. Regardless of where it's installed, it can be viewed using any web browser. We recommend using Google Chrome.


This guide covers:

Table of Contents
excludeAdditional Assistance


Logging in to your Partek Flow account will bring up the Home page (Figure 1). This page will show recent activities you've performed, recent projects you've worked on and pertinent details about each project.


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SubtitleTextPartek Flow Home page
AnchorNamePartek Flow Home page


  1. From your Partek Flow server
  2. Directly from My computer (i.e. the computer you are currently using to access Partek Flow) (500 MB limit)
  3. From a URL


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SubtitleTextUploading data into Partek Flow
AnchorNameData upload


After samples have been added and associated with valid data files, a data node will appear in the Analysis tab (Figure 3) . The Analysis tab is where you can invoke tasks and view the results of your analysis.


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SubtitleTextThe Analyses tab showing a data node of unaligned reads
AnchorNameUnaligned data node


The Analyses tab contains two elements: data nodes (circles) and task nodes (rounded rectangles) connected by lines and arrows . Collectively, they represent a data analysis pipeline (Figure 4).


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SubtitleTextExample of a data analysis pipeline
AnchorNameAnalysis pipeline


Clicking a data node brings up a context sensitive menu on the right (Figure 5). This menu changes depending on the type of data node. It will only present tasks which can be performed on that specific data type.


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SubtitleTextContext sensitive menu for unaligned reads data node
AnchorNameContext sensitive menu

Select the task you wish to perform from the menu. When configuring task options, hover over the tab to obtain additional information regarding each option (Figure 6). Click Finish to perform the task.


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SubtitleTextObtaining additional information about a task option
AnchorNameTask option information


Click the Save button on any visualization to export a publication-quality image (Figure 7).


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SubtitleTextSaving visualizations
AnchorNameSaving visualizations


Data associated with any data node can be downloaded by clicking the node and choosing Download data (Figure 8). Compressed files will be downloaded to the local computer where the user is accessing the Partek Flow server. Note that bigger files (such as unaligned reads) would take longer to download. For guidance, a file size estimate is provided for each data node. Downloaded files can be seamlessly imported in Partek® Genomics Suite®.


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SubtitleTextDownloading data
AnchorNameDownloading data


Watch a webinar of how to set-up a simple RNA-Seq project. 

Additional assistance


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