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- 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 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).
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SubtitleText | A new project with no samples in the Data Tab |
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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. 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.
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SubtitleText | Locating a text file that contains sample information |
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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).
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SubtitleText | Text with attributes |
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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.
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SubtitleText | Selecting the attributes and Sample ID |
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AnchorName | Selecting the attributes and Sample ID |
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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
).
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SubtitleText | Sample table created from a text file with attributes |
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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 must may be located in either the Partek Flow server, (Figure 2).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 both in
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server and in same directory
If the text file and the data files are both in the same directory as the Data files, 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.
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SubtitleText | Text with attributes and filenames |
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Similar to the previous section, the text file 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
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SubtitleText | The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData" |
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AnchorName | The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData" |
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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
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SubtitleText | The Current directory (red box) shows the file path to be included in a text file containing absolute paths |
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AnchorName | The Current directory (red box) shows the file path to be included in a text file containing absolute paths |
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Once you have selected the text file with filenames and/or file paths, click Next. The text file will be summarized as in Figure 7. 9. If the file types are valid, Partek Flow recognized will recognize the filenames as valid file types and was able to locate the files within the directory. The The Files column represent files to be imported.
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SubtitleText | Selecting the attributes, Sample ID and filenames |
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AnchorName | Selecting the attributes, Sample ID and filenames |
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Click
Import and the table will be created
(Figure 8). Once the table has been created, wait for . After a few seconds
and you will notice that , the server icon
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Click the Queue dropdown and select View queued tasks... to see that the files are being imported into the project the queue of import tasks (Figure 911).
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SubtitleText | Sample table created from a text file and data is queued for import |
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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, Analyses Tab will show the data node to be dark blue will appear darker (Figure 1012, right).
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SubtitleText | Analyses Tab showing data node during import (left) and once the import is completed (right) |
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AnchorName | Analyses Tab showing data node during import (left) and once the import is completed (right) |
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To view the files associated with the data, go to the Data Tab and click Show data files to expand the table. Figure 11 13 shows that 4 four files were successfully imported for each sample. You can add more or delete samples as described in the Adding samples section. Numbered figure captions |
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SubtitleText | Expanded sample table created from a text file with attributes and associated data files |
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Text file and data are in different directories
If your samples are in different subdirectories, you must include the path in for your file name. You can use either a relative path or an absolute path.
Relative paths
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 12, 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 is shown below:
/MyData/NA1031_S25_L007_R1_001.fastq.gz
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SubtitleText | The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData" |
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AnchorName | The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData" |
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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 13, 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
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SubtitleText | The Current directory (red box) shows the file path to be included in a text file containing absolute paths |
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AnchorName | The Current directory (red box) shows the file path to be included in a text file containing absolute paths |
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