The N Base Trim option allows users to trim the 3′ or 5′ end of a trace based on the number of N base calls in a selected window size.
For example, if you were to use the values of 5N bases in a window of 20 bases, PeakTrace would use a sliding window of 20 bases to scan the trace from each end and when it finds more than 5 N’s in the window the trace would be clipped. Below is an example of the N Base Trim in action. In Figure 1 a window of 20 bases is shown (coloured) and within this window only 6 N bases are present, however as the window slides a position to the right a 7th N base enters the window and the trace is trimmed and shown in Figure 2.
Figure 1. A region of a trace containing multiple N bases. The sliding window of 20 bases is coloured.
Figure 2. N Base Trimming with 7 N’s in a sliding window of 20 selected.
The N base trimming option is compatible with the set ABI limits option, which will perform a soft or “virtual” trim of low quality end regions instead of a hard trim. Combined with the N Base Threshold option users can select the minimum Q value will determine an N base being called allowing full control over the trimming.
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.