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Overview

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.
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.

Figure 1: Partek Flow Home page

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Starting a new project

From the Home Page, click the New project button. Assign a name to the project and click the Create project button

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Uploading your dataset

Upon creation of a new project, the Data tab will appear, prompting you to add samples to your project. Click the Add samples button. Selecting Automatically create samples from files is the fastest way to create a sample. Partek Flow accepts various data types including unaligned and aligned Next Generation Sequencing (NGS) reads, and microarray data. There are three ways you can upload data (Figure 2):

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• The first row lists the attribute names (e.g. Treatment, Exposure) and
• The first column of the table lists the sample names (the sample names in the file must be identical to the ones listed in the Sample name column in the Data tab)
• List the corresponding attributes for each sample in the succeeding columns

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Basic Flow Layout

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The Analysis Tab

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.

Figure 3: The Analyses tab showing a data node of unaligned reads

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Data and Task nodes

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).

Figure 4: Example of a data analysis pipeline

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Performing tasks

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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Depending on the task, a new data node may automatically be created and connected to the original data node. This contains the data resulting from the task. Tasks that do not produce new data types, such as Pre-alignment QA/QC, will not produce an additional data node.
To view the results of a task, click the task node and choose the Task report option on the menu.

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Saving visualizations

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

Figure 7: Saving visualizations

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Downloading your Data

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®.

Figure 8: Downloading data

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Want to see Partek Flow in action?

See a video of how to set-up a simple RNA-Seq project on our YouTube page:
{+}https://youtu.be/tZ4BhhVCJfU+

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Additional Assistance

If you need additional assistance, please visit partek.com/PartekSupport to submit a help ticket or find regional phone numbers to call Partek support.

Last revision: March 25, 2016

Copyright © 2016 by Partek Incorporated. All Rights Reserved. Reproduction of this material without express written consent from Partek Incorporated is strictly prohibited.