On Tue, Mar 30, 2010 at 2:56 PM, Peter <biopyt...@maubp.freeserve.co.uk> wrote: > 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. >
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? Regards, Peter C. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
