# Trimming bases and filtering reads
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 35 (Figure 2).
* Click **Finish** to run Trim bases with default settings
Figure 2. Configure the Trim bases task
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. A task and a data node are created from the Trim bases task
* 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 table and two graphs (Figure 4).
Figure 4. Results of the Trim bases task
The results are fairly consistent across samples with \~2% of reads untrimmed, \~86% trimmed, and \~12% 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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