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, allowing you to:
  • customize the name of your samples, thus avoiding 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, allowing you to:
  • combine several files into one sample
  • import data located in multiple subdirectories

This process of generating a sample table based on a text file can only be done once per project. Additional samples or attributes can still be added using the Import data or Manage attributes buttons under the Data Tab.

Select 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 and 6.

To select the text file, create a new project and in the blank Data Tab (no samples have been imported yet), click the Assign values from a file button (Figure 1). 
 

Navigate to the file using the browser as shown in Figure 2. The text file may be located in either the Partek Flow server, My computer, or from a URL.

Check the box next to the text file that you want to use and click Next.
 

Create the Sample Table

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.  (If you wish to couple the table creation with data import, you must include the filenames as described in the section below on how to Include Data Import).
 

The filenames must show the proper extensions of data types compatible with Partek Flow (see Types of Data).

Text file and data are both in server and in same directory

If the text file and the data files are both in the same directory of the Partek Flow server, 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

 

Text file and data are in different directories

If the text file and the data files are in different directories, you must modify Figure 6 to include the file paths. For text files located in the Partek Flow server, you can use relative or absolute file paths. For text files located in My Computer or URL you must use an absolute file path. (Remember that in either case, the data files must have already been uploaded in the Partek Flow server.) 

Relative path 

You can use a path relative to the location of the text file you are using to create the sample table. For example in Figure 7, the text file is located in a directory called "download" while the files are in a subdirectory called MyData, then the filenames must include the path /MyData/. An example would be: /MyData/NA1031_S25_L007_R1_001.fastq.gz

Figure 7. The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"

 

Absolute path

You can use the full path to the file based on your Partek Flow server. You must include the paths starting from the Partek Flow home directory (Figure 8, red box). For typical installations, the path begins with /home/flow/FlowData/ and so the filenames to include in the text file may look like this: /home/flow/FlowData/download/MyData/NA1031_S25_L007_R1_001.fastq.gz

Figure 8. The Current directory (red box) shows the file path to be included in a text file containing absolute paths

 

Once you have selected the text file with filenames and/or file paths, click Next. The text file will be summarized as in Figure 9. If the file types are valid, Partek Flow will recognize the filenames and locate the files within the directory. The Files column represent files to be imported.
   

Figure 9. Selecting the attributes, Sample ID and filenames

 

Click Import and the table will be created. After a few seconds, the server icon will be animated (Figure 10). This means that the process of importing data files have started. Click the Queue dropdown and select View queued tasks... to see the queue of import tasks (Figure 11).
 

Figure 10. Sample table created from a text file and data is queued for import

Figure 11. Task Queue showing import tasks for each sample

At this stage, you can also go to the Analyses Tab of the project and see that the data node has been created but the color is light blue, which indicates the import is not complete (Figure 12, left). Once all the files have been imported from the queue, the data node will appear darker (Figure 12, right).
 

Figure 12. Analyses Tab showing data node during import (left) and once the import is completed (right)

To view the files associated with the data, go to the Data Tab and click Show data files to expand the table. Figure 13 shows that four files were successfully imported for each sample. You can add or delete samples as described in the Adding samples section.
 

Figure 13. Expanded sample table created from a text file with attributes and associated data files

 

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