[EMBOSS] ABI to FASTQ with seqret

[Peter Rice]

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)

regards,

Peter R