Partek Flow Documentation

Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Issue with Pairing KB-6392 reopened

For new projects, a sample table can be automatically created from a tab-delimited text file.  There are several advantages of creating a sample table in this manner:

  • You can define multiple samples and attributes even before data has been imported, and therefore you can:
    • Customize customize the name of your samples (and not use the automatic sample names generated based on file names)
    • Import import sample sheets as defined by the instrument that generated your data
  • You can simultaneously create the sample table and import data, which allows you to:
    • Combine combine several files into one sample
    • Import import data located in multiple subdirectories

The text file must be created outside of Partek® Flow® (using other software such as Partek® Genomics Suite®, Microsoft® Excel® or any other text editor). A valid text file is a tab-delimited text file that contains at least one column that has unique entries (to be used as Sample IDs) and may have additional columns with sample information such as experimental attributes and (optional) filenames.

In a Data Tab where no samples have been imported yet (Figure 1), click the Assign sample attributes from a file button. 

 

Numbered figure captions
SubtitleTextA New project with no samples in the Data Tab
AnchorNameA New project with no samples in the Data Tab

 

Navigate to the file using the browser as shown in in Figure 2. Check the box next to the text file that you want to use and click Next.

 

Numbered figure captions
SubtitleTextLocating a text file that contains sample information
AnchorNameLocating a text file that contains sample information

 

...

Text files that contain only sample information and attributes such as the one shown in Table 1 can be imported to create a sample table with no associated files.  For this type of import, the text file may be located in either the Partek Flow serverMy computer, or from a URL (Figure 2).

 

 
Numbered figure captions
PrefixTable
SubtitleTextText with Attributes
AnchorNameText with Attributes

 

Sample nameFreezer LocationTreatmentGenotypeAge
NA1031A8Casewt15
NA1032A9Casemutant18
NA1033A10Controlwt17
NA1034A11Controlmutant17

During import, 
Partek Flow will recognize columns that contain unique entries and suggest those as possible Sample IDs.  

 You can show or hide the sample/text file columns.

In Figure 3, the headers of the text file are presented and the user can select the Sample ID, which to be imported and whether they are numeric or categorical.

 The headers from the text file are in the first column as Attribute names, which can be edited.  Example entries are shown

 

In the example in Figure 3, the columns for "Sample name" and "Freezer Location" are both unique and the radio button can be used to select the preferred sample ID.

 

...