Importing Data to the Partek Flow Projects

Data import into Partek Flow projects

After data has been transferred to the NIH Partek Flow server, the next step is to import them into a project. Sign onto Partek Flow and hit the "New project" button click to create a new project called project1. The project will then appear in the project table. Click on project1 to enter the analysis interface.

Click on the round button labeled "Add data" to begin adding data to the project.

Users will be greeted with a range of options for data import. In this example, click "Bulk" and then select "RNA-Seq". FASTQ files will be imported. Click "Next" when ready.

In the subsequent page, the current directory is displayed in the file menu on the left.

This example imports the FASTQ file in uploads/hbr_uhr_fastq. Be sure to check the box (labeled "Name") to select all files.

Scroll to the bottom of the data import page and select the data type (ie. mRNA) and click "Finish".

A rectangle labeled "Importing" will appear as data is being imported into a project.

Upon successfully importing data, there will be a circular data node in the project.

Right click on the data node to either delete this node, files, or change data type.

Next, click on the "Metadata" tab to add metadata for the samples. Under the "Sample attributes" sections, users can manually add metadata or assign it from a file. This example will demonstrate manually adding metadata by clicking on "Manage".

In the next page, select "Add new attribute".

In the dialogue box that appears, name this attribute (think of an attribute as a variable) "Treatment" so that users can distinguish the treatment group in which each sample belong. Be sure that "Categorical" is selected as this attribute type (ie. treatment group is categorical). Click "Add" when ready.

Then, under the "New category" box, enter the first treatment group (ie. HBR). Be sure to click the green "+" to add it.

After that, add the second treatment group (ie. UHR) and click on the green "+" to add. Click the "Back to metadata tab" when finishing adding treatment groups.

Hit the "Assign values" tab.

Then, select the appropriate treatment for each sample using the drop down box. Click on "Apply changes" when finished and then the "Analyses" tab to go back to the analysis.

Click on a data node to see a menu of tasks that can be performed. For instance, the first step in analyzing high throughput sequencing data from FASTQ files is to perform pre-alignment QC.