[EMBOSS] ABI to FASTQ with seqret

Peter biopython at maubp.freeserve.co.uk
Thu Apr 22 15:06:27 UTC 2010

On Tue, Mar 30, 2010 at 2:56 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Mar 30, 2010 at 2:25 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>> On 30/03/2010 14:13, Peter Rice wrote:
>>> Where do I look to find scores that we can use (and how do we convert
>>> those to phred quality scores)?
>> Aha, found something. The field is called PCON (confidence values), with
>> values 0-255.
>> There is a possibility that these could be phred scores, but I suspect they
>> are whatever the basecaller has decided to write there.
>> http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf
>> Peter R.
> Hmm. Good question - I don't know, although if they are PHRED scores
> they could go unusually high (we'd expect say 0 to 50 for a raw read).
> It could be some other encoding (e.g. scaled from 0 for a poor base to
> 255 for a perfect base). Do you have any contacts at Applied Biosystems
> to ask?
> Peter C.

Hello again Peter R (& everyone else at EMBOSS),

Did you manage to find out if the PCON confidence values in ABI files
are PHRED quality scores or not?


Peter C.

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