Why are some of my traces returned as .scf files and some as .ab1 files?
This has to do with the differences between input ABI files. The older sequencers (ABI 377 and ABI 310) do not contain all the correct fields to be able to generate a traces file with both base and quality score values. Because of the way ABI has “designed” the .ab1 file format we are not currently able to generate a valid .ab1 file from these older instrument sequencing files (the data we need just doesn’t exist in the original files). With these older style traces we output a standard .scf file as do other external basecallers like phred. This problem is not unique to PeakTrace – as far as we are aware the only other basecaller able to output .ab1 files with base quality scores is ABI’s KB basecaller. Unfortunately, the KB basecaller is not available for the older sequencers like the ABI 377 and ABI 3700. We are working on overcoming this limitation so it may be possible to generate .ab1 traces from these traces in the future.
