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Quick Video on running the Plugin
Downloading the Plugin
Download the Partek® Flow® Uploader from this link. This is a compressed zipped file
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- Click the
button. Rescanning the plugins will finish the installation and save the global configuration.
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In the Torrent Browser, you can configure a Run Plan to include the Partek Flow Uploader.
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Figure 12: Partek Flow Homepage with the new Project created by Partek Flow Uploader
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You can manually invoke the plugin from a completed run report. This allows you to export the data from the Torrent Server if you did not include the plugin in the original run plan. This also gives you the flexibility to export the same run results onto different project(s).
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- The plugin status will show Completed once the export is done and the data is available in Partek Flow (Figure 11).
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The Partek Flow Uploader plugin sends the data to the Partek Flow server. Once transferred, Partek Flow then proceeds to validate the data within a Project.
There may be some occasions when the plugin is already done transferring the data but Partek Flow is still validating it. This can easily be checked by expanding the sample table. To do so, open the project in Partek Flow, select the Data tab, and click the Show data files link on the lower left of the table (Figure 17).
Figure 17: Expanding the Sample Table to display the Data files
If the data is still being validated, the table will have empty cells in the Files column (Figure 18). Refresh the page and make sure the table is complete before proceeding.
Figure 18: Data still being validated and the project is not yet ready
Once data validation is done, the table should be complete (Figure 19).
Figure 19: All files are validated and the project is ready
If the validation fails to succeed, some files will not be imported (cells will remain blank) and there will be a notification in the Log Tab. Refer to the Run Report in the Torrent Browser to check if there was any issue in the run.
The Sample Table in Partek Flow (Figure 19) has corresponding information in the Run Report of the Torrent Browser (Figure 20).
The Sample name in Partek Flow corresponds to the Sample column in the Output files section of the Run Report. The unaligned BAM (UBAM) file for each sample has been transferred to Partek Flow and appears in the bam (Files) column. The Run Name is added as a sample attribute.
For reads that have no barcodes, the Torrent Browser does not assign a sample name (shown as None on the first row of Figure 20). These reads are also transferred to Partek Flow. For clarity, the plugin assigned them to a sample named No barcode (first row in Figure 19).
Figure 20: Torrent Browser run report showing corresponding items in the Partek Flow Sample table in red
To add multiple Runs to the same Partek Flow Project, configure the plugin and use the same Project Name (Figure 10 or Figure 15). The samples will be combined in the same project. Figure 21 shows a Partek Flow Sample table from two Ion Torrent Runs (note the Run Name column).
If two different runs have the same sample names, each would appear as a separate row with names appended (e.g., Sample 1.1).
Figure 21: Partek Flow project containing data from multiple runs. Duplicate samples are appended by a dot followed by a number
Samples you do not wish to include in your analysis (particularly those with no barcodes) can be easily deleted by clicking the gear icon next to the sample name and selecting Delete sample (Figure 22).
Figure 22: Deleting samples in Partek Flow
The data transferred by the Partek Flow Uploader is stored in a directory created for the Project within the user's default project output directory. For example, in Figure 19, the data for this project is stored in:
/home/flow/FlowData/jsmith/Project_CHP Hotspot Project
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The plugin transfers the Unaligned BAM data from the Torrent Browser. The UBAM file format retains all the information of the Ion Torrent Sequencer. In the Partek Flow Project, the Analyses tab would show a circular data node named Unaligned bam. Click on the data node and the context-sensitive task menu will appear on the right (Figure 23).
Unaligned BAM files are only compatible with the TMAP aligner, which can be selected in the Aligners section of the Task Menu. If you wish to use other aligners, you can convert the unaligned BAM files to FASTQ using the Convert to FASTQ task under Pre-alignment tools.
Some information specific to Ion Torrent Data (such as Flow Order) are not retained in the FASTQ format. However, those are only relevant to Ion Torrent developed tools (such as the Torrent Variant Caller) and are not relevant to any other analysis tools.
Figure 23: Analyses tab of Partek Flow showing the task menu available for the selected Unaligned BAM file data node
Once converted, the reads can then be aligned using a variety of aligners compatible with fastq input (Figure 24) . You can also perform other tasks such as Pre-alignment QAQC or run an existing pipeline.
Another option is to include the Convert to FASTQ task in your pipeline and you can invoke the pipeline directly from an Unaligned bam data node.
Figure 24: Unaligned reads in the FASTQ format are compatible with more tasks
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Deleting data in Partek Flow can be done by deleting the project. During project deletion, you will be given an opportunity to delete data. These include the data transferred by the Partek Flow plugin (Input Files) and the data generated by any Task within Partek Flow (Output Files). Deleting data in Partek Flow does not delete any data in the Torrent Browser.
There are a couple of ways to delete a project. From the Partek Flow home page, click the delete icon under the Actions column (Figure 10). You can also have the project open and click the gear icon on the top right of the page and select Delete project (Figure 25).
Figure 25: Deleting an open project in Partek Flow
A page displaying all the files associated with the project appears. Click the triangle to expand the list. Select the files to be deleted from the server by clicking the corresponding checkboxes next to each file (Figure 26). By default, all Output files generated by the project are selected. The Input files list all the data uploaded by the plugin.
Figure 26: Expanded selection of files to be deleted in with one file being shared by another project
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Overview
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