Based on pre-alignment QA/QC, we need to trim low quality bases from the 3' end of reads. 

• Select the Unaligned reads data node
• Select Trim bases from the Pre-alignment tools section of the task menu (Figure 1) 
  
  

Figure 1. Invoking Trim bases task

We will configure Trim bases to remove base pairs from the 3' end of reads until it reaches a base pair call with a Phred score of equal to or greater than 20. Hover over any  to get additional information about a specific option. 

• Set Trim based on to Quality score
• Set End min quality level (Phred) to 20 
• Set Trim from end to 3-prime (right end)
• Leave Advanced options set to default
• Select Finish (Figure 2)
  

Figure 2. Configuring the Trim bases task

The Trim bases task will generate a new data node, Trimmed reads. While tasks have been queued or are in progress they have a lighter color. Any output nodes that the task will generate, such as the Trimmed reads data node from the Trim bases task, are also displayed in a lighter color until the task completes. Once the task begins running, a progress bar is displayed on the task node (Figure 3). 

• Select the Trimmed reads data node
• Select Task report from the task menu

The report shows the percentage of trimmed reads and reads removed in a spreadsheet (Figure 4) and a graph (Figure 5).  

Figure 4. Spreadsheet showing results of the Trim bases task

Figure 5. Bar chart showing results of Trim bases task

The average quality score for each base call at each position for each sample is also shown as a graph (Figure 6).

Figure 6. Updated base call quality graph after Trim bases task

The results are fairly consistent across samples with ~65% of reads untrimmed, ~30% trimmed, and ~5% removed for each. 

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