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.
Figure 3. Task and Data nodes that have been queued or are in progress are shown in a lighter color than completed tasks.
- 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 ~50% of reads untrimmed, ~45% 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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