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The Partek® Flow® software provides a built-in Large File Viewer to preview files generated by tasks within a project. The file types supported by the viewer are:
.bam | .sam | .bgx |
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The preview will display up to the first 1000 lines.
This feature of Partek Flow is one of the ways the software provides access to your own data. Remember that in Partek Flow, you can also download any data node through the context-sensitive menu (select a data node and choose Download data from the menu). Furthermore, any table from a Task Report can be downloaded by selecting the Download hyperlink at the bottom right of each table.
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Previewing a File from the Task Details
The way to access the viewer is through the Task details page. Select a rectangular task node and choose the Task details in the context-sensitive menu (Figure 1). You can also access the Task details from the bottom of any Task report.
Figure 1: Opening the Task details
The Output files section of the Task details page shows the different files generated by the task (Figure 2).
Figure 2: Selecting an output file to preview from the Task details
Note that since some filenames created by Partek Flow are generated by appending the filename of an input file, files may contain several file name extensions. The last extension is the actual file format for the file. In the example in Figure 2, the file in the first row (SRR1020608.fastq.bam) is a BAM file generated from a FASTQ file.
To open the Large File Viewer, click the name of the output file and select from the viewing options (Figure 3), which depends on the data type selected.
Note that only files listed in the first section of this document are compatible with the viewer. If you select a file from the table that is not compatible (such as a zip file), the file will not be not previewed, but would be downloaded to your local drive.
Once you have made your selection from the radio buttons (Figure 3), click View Data. You also have the option to Download the selected file instead of previewing it.
Figure 3: Choices when viewing a BAM file
For raw data, the Large File Viewer will display an Output file preview in a scrollable window showing up to 1000 lines (Figure 4). The filename, filesize, and the name of the task that generated the file are also displayed.
Figure 4: Output file preview for viewing raw data
For BAM files, additional options are to display the headers that were generated by the aligners (Figure 5) and the samtools flagstat summary statistics (Figure 6).
Figure 5: BAM header preview
Figure 6: Simple stats (samtools flagstat) for a BAM fileAnchor
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Previewing an Imported File
There may be situations when you wish to preview files that were originally imported into a project. However the first data node in project (known as the origin data node) does not have any task details associated with it in the context-sensitive menu (Figure 7).
Figure 7: The origin data node does not have task details in the context-sensitive menu
To access the task details in an import task, go to the Log tab of the project and select the Import task in the table (Figure 8). Select the top level task Import (and not the Import unaligned reads).
Figure 8: The log tab showing the Import task
Selecting the Import from the Log table reveals the Task details and the file that was successfully imported (Figure 9). Note that even though the file has just been imported, it is placed under the Output files section because it has already gone through the import process of file validation and other file checks.
Figure 9: Task details of an Import task
To open the Large File Viewer, simply select the filename of the file you wish to preview as explained in the previous section.
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Additional Assistance
If you need additional assistance, please visit partek.com/PartekSupport to submit a help ticket or find regional phone numbers to call Partek support.
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Last revision: March 29, 2016
Copyright © 2016 by Partek Incorporated. All Rights Reserved. Reproduction of this material without express written consent from Partek Incorporated is strictly prohibited.
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