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
Selection of the Text File
The text file must be created outside of Partek® Flow® (you can use software such as Partek® Genomics Suite®, Microsoft® Excel® or any text editor). A valid text file is a tab-delimited text file that contains one sample per row and columns containing sample information. At least one column must have unique entries and will be suggested as Sample IDs. Additional columns may contain numeric or categorical attributes and (optional) filenames. Examples of text files are shown in Figures 3, X, Y, Z.
To select the text file, create a new project and in the blank Data Tab (no samples have been imported yet), click the Assign sample attributes from a file button (Figure 1).
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. The text file may be located in either the Partek Flow server, My computer, or from a URL. However, if you wish to create the sample table and start importing the data at the same time, (explained later in this section), the text file must be on the Partek Flow server.
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
Creating a Sample Table without Data Import
Text files that contain only sample IDs and attributes such as the one shown in Figure 3 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).
Figure 3. Text with Attributes
The text file will be summarized as in Figure 4. The first two columns show the headers and example terms parsed from the text file in Figure 3. The suggested attribute names can be renamed before import. Columns that contain unique entries are recognized as possible Sample IDs and can be selected using the radio button. You can choose which attributes to be included and, if applicable, whether they are numeric or categorical. The Show/hide file preview link allows you to preview the text of the tab delimited text file you are using.
In the example in Figure 4, the columns for "Sample name" and "Freezer Location" are both unique and the former is selected as the Sample ID. The "Freezer location" has been deselected and it will not be included in the resulting Sample table. Since "Age" has all number terms, the Attribute type column for it is a drop down menu to choose between Numeric and Categorical. There are no filenames in the text file so the Files column is empty.
Figure 4. Selecting the attributes and Sample ID
Click Import and the table will be created (Figure 5). Click Show data files to expand the table and associate files. For more details see the Adding samples section.
Figure 5. Sample Table created from a Text File with Attributes
Creating a Sample Table with Data Import
If you have a text file that contains sample IDs and attributes as well as the filenames of your data, you can create the sample table and start the data import at the same time. This is particularly useful for projects where multiple files are associated with the same sample (e.g., a sample ran in multiple lanes in the sequencer). For this type of import, the text file must be located in the Partek Flow server (Figure 2).
In the text file, each filename to be associated with the sample must be separated by a tab. That means, if you are using a spreadsheet software to generate the text file, there is a maximum of one file per column. You also need to add headers such as file1, file2, etc., to define the columns. There is no limit on the number of columns on the text file.
The filenames must show the proper extensions of data types compatible with Partek Flow (see Types of Data).
The actual files can be in the same directory as the text file or in a different directory. If the files are in a different directory, you must include the file paths.
Text file and data are in the same directory
If the text files are in the same directory as the Data files, simply include the filenames in the text file as shown in Figure 6. You do not have to specify the file path.
Figure 6: Text with Attributes and Filenames
The text file will be summarized as in Figure 7. Filenames that are recognized as valid file types and also located in the same folder as the text file are presented in the Files column.
Figure 7. Selecting the attributes, Sample ID and filenames
Click Import and the table will be created (Figure ). Click Show data files to expand the table and associate files. For more details see the Adding samples section.
Figure 8. Sample Table created from a Text File and files are queued up for the import
Figure 9. Task Queue showed each file is queued for import
Figure 10. Sample Table created from a Text File with Attributes and associated imported Files
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
Issue with Pairing KB-6392 reopened
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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Figure 6. Text with Attributes
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