Trim Bases

The Trim bases task is used to trim bases from the 5'-end or 3'-end of the reads. The most obvious reason for Trim bases is to trim away poor quality bases from the read prior to alignment because these can potentially affect alignment rate.

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Advanced options

In some cases, the reads that result from base trimming can have very short read lengths and thus are not recommended for alignment.Thus, Partek^® Flow^® Flow provides the option to set a Min read length after base trimming. This discards reads that are shorter than the set length. 

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Trim Bases Task Details Page

The Task Details page for Trim bases can be accessed by selecting the task node Trim bases, and subsequently selecting Task Details from the Task results section. In the Task details page, several sections are available:

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• Command Lines: shows the commands used for running Trim bases function by the software Partek Flow

Trim Bases Task Report Page

The Trim bases Task Report page can be accessed by selecting either the Trim bases task node or Trimmed reads data node and then selecting the Task Report from the Task results section of the task pane. There is a link at the bottom of the page to directly go to the Task Details page. The page displays the following components:

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• Average base quality score per position of trimmed reads: shows the average base quality score at each position of the trimmed reads for all samples in the project.

Trim Bases Output Files

The Trim bases function produces trimmed unaligned reads which is named as Trimmed Reads data node. The Trimmed Reads node will have the "trimmed" word appended to the filename. The Trimmed Reads data can be downloaded by selecting the Trimmed Reads node and then select Download data from the task pane. However, if you have access to the Partek Flow server, you can go to the Task Details page and identify the location of the output files from the Output Files section as described on the Trim Bases Task Details section above. The Trimmed Reads data node will have the same format as the raw data.

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