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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).

The implementation of Layers makes optimizations easy and organized. Instead of creating separate nodes in a pipeline, another set of nodes with a different color is stacked on top of previous analyses (Figure 34). To see the parameters that were changed between runs, hover the mouse icon over the set of stacked task nodes and a pop-up balloon will display them. The text color signifies the layer corresponding to a specific parameter.

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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.

To select a different layer, use the left mouse button to click on any node of the desired layer. All the nodes associated with the selected layer have the same color and when clicked will be displayed on the top of the stack.

Downloading Data

Data associated with any data node can be downloaded using the Download data link in the task pane (Figure 2). 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. These zipped files can easily be imported by the Partek^® Genomics Suite^® software.

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