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 the name of your samples (and not use the automatic sample names generated based on file names)
- 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 several files into one sample
- 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.
In a Data Tab where no samples have been imported yet (Figure 1), click the Assign sample attributes from a file button.
Figure 1. A 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.
Figure 2. Locating a text file that contains sample information
Depending on the content and location of the text file, creating the sample table can be done with or without data import.
Creating a Sample Table without Data Import
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 server, My computer, or from a URL (Figure 2).
Table 1. Text with Attributes
During import, Partek Flow will recognize columns that contain unique entries and suggest those as possible Sample IDs.
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.
Figure 3. Selecting the attributes and Sample ID
You can also unselect the columsn you do not wish to import
Text can be imported as categorical attributes
Numeric can be imported as smaple attributes
You can rename the header.
Click import and the table will be created
Each row is now a sample but is not associate with any file. Click Show data files to expand the table and associate files. For more details see the relevant section here.
Creating a Sample Table with Data Import
A feature of creating the sample ability to combine this step with data import ... the additional feature of importing samples during table creation (described below) are currently only available if the text file is in the Partek Flow Server.
can only be at the same time as creating the sample table) can only be performed if
a sample table that also includes the locations of filenames can only be based on the sample table (as described later in this section)
The text file must be in the server or a folder that is readable by the partek flow server. the text file contains filenames
A valid text file:
TABLE TEXT FILE NO PATH
useful if there are many files for one sample, You can add as many columns as you want on the right
Flow recognizes sees that some columns in your text file are filenames of
FIGURE OF NAVIGATION... SHOW THAT THE DATA IS IN THE SAME DIRECTORY MYDATA
FIGURE WITH FILENAMES
FIGURE RESULTING TABLE
FIGURE IMPORT task
FIGURE EXPANDED TABLE
In the example above, the text file and Data files are in the same directory. If your samples are in different subdirectories, YOU CAN USE PATHS. RELATIVE OR ABSOLUTE
Relative path
FIGURE NAVIGATION... SHOW THAT THE DATA IS DIFFERENT DIRECTORY THAN MY DATA
TABLE RELATIVE PATH
Relative to the text file
Absolute path
FIGURE NAVIGATION SHOW THAT THE DATA IS IN DIFFERENT DIRECTORY AND the directory structure starts with /home/directory....
TABLE ABSOLUTE PATH
you must write the path this way
For a short video of using a text file, please see. the
Note that this can only be done on a blank project... once you have any import
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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