PeakTrace Online (the free version of PeakTrace) has always used a very basic group of settings. One area that can cause it problems are traces with weak signal at the end of the trace. This is because PeakTrace Online was using any of the trace trim settings. While it should not really matter, some people get worried when seeing a large number of low quality base calls at the end of the trace. Personally I would rather have a low quality call rather than no call at all, but many people prefer these low quality regions removed.
To avoid this I have changed the online settings so that PeakTrace now uses the window quality score trimming options. PeakTrace Online will now trim any region where the average quality score in a 20 base window drops below 12 (i.e. -wq 12 20).