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

• Click the Unaligned reads data node
• Click Pre-alignment tools in the task menu
• Click Trim bases (Figure 1) 
  
  

Figure 1. Invoking the Trim bases task

By default, Trim bases removes bases starting at the 3' end and continuing until it finds a base pair call with a Phred score of equal to or greater than 20. Hover over the  for additional information on any task option (Figure 2). 

• Click Finish to run Trim bases with default settings
  

Figure 2. Viewing additional information about the Quality score trimming method

The Trim bases task will generate a new data node, Trimmed reads (Figure 3). We can view the task report for Trim bases by double-clicking either the Trim bases task node or the Trimmed reads data node or choosing Task report from the task menu. 

• Double-click the Trimmed reads data node to open the task report

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

Figure 4. Results of the Trim bases task

The results are fairly consistent across samples with ~65% of reads untrimmed, ~30% trimmed, and ~5% removed for each. The average quality score for each sample is increased with higher average quality scores at the 3' ends. 

• Click RNA-Seq 5-AZA to return to the Analyses tab

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