The q average trim option allows you to select a quality score average clipping threshold and window size, so that traces are clipped at their 5′ and 3′ ends when the average quality score in a sliding window of defined base number falls below the clipping threshold. The default values are a quality score average clipping threshold of 12, and a sliding window of 20 bases. This means that by default, all traces are clipped when the average quality score falls below 12 within a window of 20 bases.
This option is especially useful for removing low quality regions at the 5′ and 3′ ends of your traces. Figure 1 shows an unclipped trace with a poor quality 3′ region and Figure 2 shows the same trace processed using the q average trim to remove the low quality region.
Figure 1. An unclipped trace showing a poor quality 3′ region.
Figure 2. The same trace as in Figure 1, but trimmed with the Q average trim function. Selected parameter values were an average clipping threshold of 15, a sliding window of 20 and the trim 3′ end only function toggled on.
The q average trimming option is compatible with the set ABI limits option, which will perform a soft or “virtual” trim of low quality end regions.
If you have untrimmed traces that have already been processed through PeakTrace and you would like to trim them without being charged more units, you can perform post-process trimming by selecting abi/kb as the basecaller and choosing the appropriate trimming method. Remember to turn off the clean baseline, extra baseline and extra normalization options or else you will be charged for trimming the traces.