*Auto Trim*

1. Click ‘Auto Trim All’ to trim all .ab1 files incorporated into your project.

**Note:** This will use an automatic method to trim low-quality base calls (i.e., Phred score of 20 or below) from the 5’ and 3’ ends of your sequence(s).

*Manual Trim*

**Note:** Only files with trace data (i.e., .ab1 files) will be available in the dropdown menu.

1. Under ‘Select a sequence to trim,’ choose an individual sequence using the dropdown menu.

**Note:** Undetermined bases are designated as ‘n.’ Lower-quality base calls are shown as lowercase nucleotides, while higher-quality base calls are shown as uppercase nucleotides.

2. Click on the nucleotide at the point where you wish to trim at the 5’ (beginning) of the sequence. The trace file at that position will be displayed in the ‘ABI Viewer’ inset. A thin strikethrough line will also appear, indicating which nucleotides will be trimmed.
3. Click on the nucleotide at the point where you wish to trim at the 3’ (end) of the sequence. The trace file at that position will be displayed in the ‘ABI Viewer’ inset. A thin strikethrough line will also appear, indicating which nucleotides will be trimmed.
4. When you have selected the desired nucleotides to trim, click ‘Save Trim.’

**Tip:** Click ‘Clear Selection’ to undo your selections. Click ‘Revert to Original’ to restore any trims made previously, including those made with the Auto Trim feature. Click ‘View Suggested’ to view a suggested set of nucleotides to trim based on their quality.