...

Multiple data files can be compressed a single .zip file before uploading. Partek Flow will automatically unzip the files and put them in the upload directory.

...

Once a sample is created in a project, the files associated with it can be modified. In the expanded view, mouse over the +/- column of a sample. The highlighted icons will correspond to the options for the sample on that row.

...

Create a new blank sample

...

Adding Files to an existing project

...

Importing feature counts

...

Otherwise, manually specify the orientation of the data matrix by changing the Input format drop-down menu (Figure 10). If the data has been log transformed, specify the base under Counts format.

...

Project output directory

...

Individual categories for the attribute must then be entered. Enter a name of the New category and click Add. The Name of the new category will show up in the table. The category can also be edited by clicking or deleted by clicking . Additionally, sub-categories can be added by clicking in the Options column. After all the categories have been added to this attribute, click Close to proceed.

...

Adding a numeric attribute

...

Adding a system-wide attribute

...

Assigning categories or values to attributes

...

When all the attributes have been entered, click Apply changes and the sample management table will be updated. After editing the sample table, make sure there are no fields with blank or N/A values before proceeding. To rename or delete attributes, click Manage attributes from the Data tab to access the Manage attributes page. Note that you cannot delete an attribute if a sample is assigned to it.

...

The first row of the table in the text file contains the attributes (as headers). The first column of the table in the text file, regardless of the header of the first column, should contain either the sample names or the file names of the samples already added in Partek Flow. The first column is the unique identifier that will match the samples to the correct values or categories.

...

You can change the name of a specific attribute by editing the Attribute name text box. Columns containing letter characters are automatically selected as categorical attributes. Columns containing numbers are suggested to be numeric attributes and can be changed to categorical using the drop down menu under Attribute type.

...

You can download your completed Sample management table by clicking the Download link at the lower corner of the table. This will export a tab-delimited text file with contents of the table.

...

Data and Task nodes

...

Task nodes (Figure 22) represent the analysis steps performed on the data within a project. For details on the tasks available in Partek Flow, see the specific chapters of this user manual dedicated to the different tasks.

...

Only the tasks that are available for the selected data node will be listed in the menu. For data nodes, actions that can be performed on that specific data type will appear.

...

Running a task

...

Tasks that are currently running (or scheduled in the queue) appear as translucent nodes. The progress of the task is indicated by the progress bar within the task node. Hovering the mouse pointer over the node will highlight the related nodes (with a thin black outline) and display the status of the task (Figure 26).

...

Canceling and deleting tasks

...

Cancelled or failed tasks are flagged by small red circles with exclamation points on the tasks nodes. Data nodes connected to incomplete tasks are also incomplete as no output can be generated (Figure 28). For failure due to errors, see the Task details.

...

To delete tasks from the project click the right mouse button on the task node and then select Delete (Figure 29). Alternatively, click the task node and select Delete task from the task pane. The nodes downstream of this task will be deleted. However, deleting the output files is optional (Figure 28, inset).

...

Task Results and Task Actions

...

Items from the Task results section inform on the action performed in that node. Certain tasks generate a Task report (Figure 31), which include any tables or charts that the task may have produced.

...

The Task details shows detailed diagnostic information about the task (Figure 32). It includes the duration and parameters of the task, lists of input and output files, and the actual commands (in the command line) that were run.

...

Additionally, the Task details page would contain the error logs of unsuccessful runs. The user can download the logs or send them directly to Partek. This page plays an important role in diagnosing and troubleshooting issues related to task.

...

Layers

It is common for next-generation sequencing data analysis to examine different task parameters for optimization. Users may want to modify an upstream step (e.g. alignment parameters) and inspect its effect on downstream results (e.g. percent aligned reads).

...

Layers are formed when the same task is performed on the same data node more than once. They are also formed when a task node is selected and the Re-run it w/new parameters is selected in the task pane. This will allow the users to change the options only for the selected task. The user may choose to re-run the task to which the changes have been made, as well as all the downstream tasks until the analysis is completed. To do so, select Re-run w/new parameters, downstream tasks from the task pane.

...

The Log Tab

...

Each row of the table corresponds to a task node in the Analyses tab. The list can be sorted according to a specific column using the sort icon .

...

Project Management

...

When deleting a project, the project will be deleted from the Partek Flow instance. In addition, the user is also given the choice to delete the output files produced by the project.

...