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) 
  
  

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)
  

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).  

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

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