On Tue, Mar 30, 2010 at 2:25 PM, Peter Rice <p...@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. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss