[EMBOSS] ABI to FASTQ with seqret
Peter Rice
pmr at ebi.ac.uk
Tue Mar 30 13:13:28 UTC 2010
On 30/03/2010 12:46, Peter 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.
We have code to extract various fields from ABI trace files, but I'm not
familiar with the details fo the format, and documentation appears hard to
find.
Where do I look to find scores that we can use (and how do we convert those
to phred quality scores)?
regards,
Peter
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