On 2011-09-16, at 5:34 PM, Bastien Chevreux wrote: > On Friday 16 September 2011 23:23:36 John Nash wrote: > > [...] > > Who do you trust? > > You should forget about the native pregap basecaller. Many sequencing centers > I know used phred as part of the pregap package (there either was an import > module or they wrote one, I do not recall). > > In the company I previously worked for we had a licence for TraceTuner and it > actually did a slightly better job compared to phred, but that is 10 years > ago. > > Note: the qualities for the sequences you posted look funny for the > TraceTuner called sequence ... they are in the low 0 to 10s and rarely above, > while phred is in the 30s for large parts, which is more what I'd expect. You > might want to check the options with which you called TT. Thanks Bastien. I used the defaults for ttuner via command line. The java package crashes on my Mac and Ubuntu boxes (no Windows here), so I used the command line version where the quality options are sparse. I think I'll stick with phred as I am used to it. Have a good weekend. John