...

• You can define multiple samples and attributes even before data has been imported, and therefore allowing you canto:
  • customize the name of your samples (and not use , 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, which allows 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, X, Y, Z 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 sample attributes values from a file button (Figure 1). 
 

...

...

...

 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.
 

...

...

Image Removed

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. 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 (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).
 

Numbered figure captions
SubtitleText Text with

...

attributes AnchorName Text with

...

attributes

...

Image Added

...

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 andinclude 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.
 

Numbered figure captions
SubtitleText Selecting the attributes and Sample ID AnchorName Selecting the attributes and Sample ID

...

Image Added

...

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).
 

Numbered figure captions
SubtitleText Sample

Table

table created from a

Text File

text file with

Attributes

attributes AnchorName Sample

Table

table created from a

Text File

text file with

Attributes

attributes

Image Removed

Image Added

 

Creating a Sample Table with

Include 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

...

may be located in either the Partek Flow server, 

...

My computer, or from a URL. However, the data files should already be uploaded to the Partek Flow server (see section on file transfers). 
 

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. It is also possible to have a different number of files associated with different samples.

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.

Image Removed

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.

Image Removed

...

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.
 

Numbered figure captions
SubtitleText Text with attributes and filenames AnchorName Text with attributes and filenames
Image Added

 

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

Numbered figure captions
SubtitleText The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData" AnchorName The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"
Image Added

 

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

Numbered figure captions
SubtitleText The Current directory (red box) shows the file path to be included in a text file containing absolute paths AnchorName The Current directory (red box) shows the file path to be included in a text file containing absolute paths
Image Added

 

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.
 

Numbered figure captions
SubtitleText Selecting the attributes, Sample ID and filenames AnchorName Selecting the attributes, Sample ID and filenames
Image Added

 

Click Import and the table will be created. After a few seconds, the server icon will be animated (Figure 10).  Click Show data files to expand the table and associate files. For more details see the Adding samples section.

 

 

 

Image Removed

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

...

Rate Macro
allowUsers false

Numbered figure captions
SubtitleText Text with Attributes AnchorName Text with Attributes

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).
 

Numbered figure captions
SubtitleText Sample table created from a text file and data is queued for import AnchorName Sample table created from a text file and data is queued for import
Image Added

Numbered figure captions
SubtitleText Task Queue showing import tasks for each sample AnchorName Task Queue showing import tasks for each sample
Image Added

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).
 

Numbered figure captions
SubtitleText Analyses Tab showing data node during import (left) and once the import is completed (right) AnchorName Analyses Tab showing data node during import (left) and once the import is completed (right)
Image AddedImage Added

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.
 

Numbered figure captions
SubtitleText Expanded sample table created from a text file with attributes and associated data files AnchorName Expanded sample table created from a text file with attributes and associated data files
Image Added

 

Additional assistance

Rate Macro
allowUsers false