Quick Start Guide

Overview

This guide outlines 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:

• Overview

• Starting a new project

• Basic Partek Flow layout

• Saving visualizations

• Downloading your data

• Viewing task details

• Additional navigation

• Access tutorial data from the interface

• Partek Flow in action

Logging in to your Partek Flow account will bring up the Home page. This page shows recent projects you've worked on and pertinent details about each project. Click the project name to open the project and continue the analysis.

Access projects from the homepage by clicking on the project name

Starting a new project

From the Home Page, click the Add project button.

Click the Add project button to start a new project

Assign a name to the project and click the Create project button.

Name the project and click Create project

Uploading your dataset

Upon creation of a new project, the Analyses tab will appear, prompting you to add samples to your project.

Click the blue Add data button

Select the type of data (Single cell, Bulk, Other), choose the assay type, and select the data format for the files you would like to create samples from. Partek Flow accepts various data types. Use the Next button to proceed with import.

There are three ways you can upload the data:

1. From your Partek Flow server (click here for more information)

2. From a URL

3. From a GEO / ENA Bioproject (click here for more information)

Because genomics datasets are generally large, it is ideal to have the data copied in a folder directly accessible to the Partek Flow server. Make sure that the directory has the appropriate permissions for Partek Flow to read and write files in that folder. You may wish to seek assistance from your system administrator in uploading your data directly.

Basic Partek Flow layout

The Metadata Tab

Once the samples have been created, assign the corresponding sample attributes for each sample using the Metadata tab.

Sample and cell attributes are managed in the Metadata tab

The most efficient way to assign sample attributes is by clicking Assign sample attributes from a file and uploading a tab delimited text file. The file should contain a table with the following:

• 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 Metadata tab)

• List the corresponding attributes for each sample in the succeeding columns

If you already have attribute information about your cells from a single cell experiment, you can use the Annotate cells task in the Analyses tab of Partek Flow to apply this information to the data. Please click here for more information on adding a priori cell annotation. Once applied, these can be used like any other attribute in Partek Flow, and thus can be used for cell selection, classification and differential analysis. Data nodes in the Analyses pipeline that contain this cell level information (e.g. Graph-based clusters data node) can be published to the project and will then be available to Manage under Cell attributes. Please click here for more information on publishing cell attributes to the project.

The Analyses Tab

After samples have been added and associated with valid data files, a data node will appear in the Analyses tab. The Analyses tab is where you can invoke tasks, using the toolbox on the right, and view the results of your analysis.

To add more data, use the context sensitive menu on the right (toolbox) and choose Add data under Import. There is also an option in the Metadata tab to Add data.

Data can no longer be added to the project once the analyses begins and tasks are performed from the initial data node.

The Analyses tab showing a data node of unaligned reads. Use the Context-sensitive menu on the right to run tasks.

Data and task nodes

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

Example of a data analysis pipeline

Performing tasks

Clicking a data node brings up a context sensitive menu on the right. This menu changes depending on the type of data node. It will only present tasks which can be performed on that specific data type. Hover over the task to obtain additional information regarding each option.

Use the context sensitive menu to run a task on the data node

Select the task you wish to perform from the menu. When configuring task options, additional information regarding each option is available. Click Finish to perform the task.

Configure the task options to meet your needs and click Finish

When available, hover over Tooltips or click the video help for decision making.

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 data node and choose the Task report option on the menu.

Saving visualizations

Some visualizations are available in the task report and others are sent to the Data viewer for modification and export.

Save visualizations from a task report

Click Save on any visualization to export a publication-quality image.

Save visualizations using the save icon

Save visualizations from the Data viewer

To save an individual image within the Data viewer to your machine, click Export image in the top right corner of the image and select the format, size, and resolution then click Save.

Click export image to Save the image in different formats, sizes and resolutions

For more information on using the Data viewer please click here.

Downloading your data

Data associated with any data node can be downloaded by clicking the node and choosing Download data at the bottom of the task menu. 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.

Select the data node and navigate to the bottom of the task menu then click Download data

Viewing task details

There are three ways to view details about the tasks performed in Partek Flow.

• Click the individual task node (rectangle) and select Task details from the task menu

• Click the data node (circle) and select Data summary report from the task menu

• Click the Log tab

View individual task details

This is used to view the task details from an individual task, including the commands. Navigate to the the task node (rectangle) and select Task details from the task menu.

Select the task node (rectangle) and click Task details to view information about the task including the commands

View task details for all performed tasks upstream of the data node

This is used to access the task details for all of the steps performed upstream from the data node that has been selected. Click the data node (circle) and select Data summary report from the task menu.

Select the data node (circle) and click Data summary report to show information for all upstream tasks

Please click here for more information on the Data summary report

View all tasks performed on the project

The Log tab is used to view all tasks performed within the project. It contains a table of the tasks that are running, scheduled, or those that have been completed within the Partek Flow. It provides an overview of the task progress, enables task management, and links to detailed reports for each task.

The Log tab is used to view all tasks within the project and enables task management including task progress and links to detailed reports for each task

Please click here for information about the Log tab.

Additional navigation

Project settings tab

To modify the name of the project and other details like adding collaborators, navigate to the Project settings tab.

Navigate to the Project settings tab to modify the name of the project and other details like adding collaborators

Please click here for information about the Project settings tab.

Task node actions

Task node (rectangle) actions on the task menu (toolbox) allow you to rerun tasks, rerun with downstream tasks, edit the description, and change the color.

Click the task node (rectangle) to perform task actions in the toolbox (task menu)

Please click here for more information on Task actions.

Pipelines

Pipelines can be created for future use. Select Create new pipeline near the bottom left-hand side of the browser window. Please click here for a tutorial which covers saving and running a pipeline.

Pipelines can be created for future use by clicking Create new pipeline

Please click here for more information about Pipeline management.

Access tutorial data from the interface

Partek Flow also provides demo data within the interface so you can automatically begin a project with this data type for bulk RNA-Seq or single cell RNA-Seq and follow along with the tutorials listed below. Navigate to your avatar in the top right corner and click Settings then click the data type of interest.

• Bulk RNA Seq (RNA-Seq 5-AZA)

• Single cell RNA-Seq (Single cell glioma (multi-sample))

Navigate to the tutorial data by clicking your Avatar, Settings, then the data of interest

Partek Flow in action

Watch live training event recordings for different types of data.

Additional Assistance

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