On Tue, Mar 30, 2010 at 1:02 PM, Peter Rice <[email protected]> wrote: > > On 30/03/2010 12:46, Peter C. wrote: >> >> Hi all, >> >> I've got some "Sanger" capillary sequence files in ABI trace file >> format, which I understand includes the probabilities of the 4 bases >> along the sequencing run. I'd like to extract this as a FASTQ file >> with meaningful quality scores based on the trace data (for use in >> assembly). >> >> This doesn't seem to work - the FASTQ quality score characters are all >> double quotes (ASCI 34), meaning PHRED quality 1. > > I will take a look. I don;t recall anyone using the quality scores from ABI > data when we first imeplemented it (at that time Staden Experiment files > were the only supported output format with any quality scores) >
Thanks Peter, Regarding other possible tools, there is the obvious choice of PHRED (although getting a copy is non-trivial), and based on this thread: http://seqanswers.com/forums/showthread.php?t=3165 I've just tried TraceTuner 3.0.6beta which is open source (specifically, GPL v2 or later): https://sourceforge.net/projects/tracetuner/ With the ttuner -nocall option to reuse the sequence as-is from the ABI file results in zero quality scores. Allowing ttuner to re-call the bases (the default), it can output FASTA/QUAL/PHD with meaningful qualities (from which I can easily make a FASTQ file). Peter C. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
