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SubtitleText | Text with attributes and filenames |
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AnchorName | Text with attributes and filenames |
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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 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.
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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. 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).
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SubtitleText | Sample table created from a text file and data is queued for import |
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AnchorName | Sample table created from a text file and data is queued for import |
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SubtitleText | Task Queue showing import tasks for each sample |
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AnchorName | Task Queue showing import tasks for each sample |
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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, the data node will appear darker (Figure 12, 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 13 shows that four files were successfully imported for each sample. You can add or delete samples as described in the
Adding samples section.
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SubtitleText | Expanded sample table created from a text file with attributes and associated data files |
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AnchorName | Expanded sample table created from a text file with attributes and associated data files |
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