[EMBOSS] ABI to FASTQ with seqret

[Peter]

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.