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)
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
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.
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