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A Bowtie alignment task will be used as an example, but the steps are the same for any task that allows configuration of advanced settings.
Click Configure in the Advanced options section on the Task setup page (Figure 1).
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Name the new custom option set, add a description (optional) and click Save in the New option set dialog (Figure 3).
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User-defined command lines can be copied and pasted to create a custom option set.
This is particularly useful if, for example, you have previously run an alignment with custom options on the command line and wish to use the same set of options for an alignment in Partek Flow.
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