On Thu, Apr 22, 2010 at 4:22 PM, Peter Rice <[email protected]> wrote: > > On 22/04/2010 16:06, Peter C. wrote: > >> 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? > > Yes ... and maybe. > > The first scores are written bu the ABI basecaller. > > A second set can be written by any basecaller. These may be phred quality > scores but could in theory be anything. > > EMBOSS will assume they are phred scores as there is no way to tell > otherwise. > > regards, > > Peter Rice
Does this mean there is an updated seqret in a public repository where I can convert an ABI file to FASTQ taking the ABI basecaller's sequence and PHRED scores? I'd be interested to test that... or a patch against EMBOSS 6.2.0. Thanks, Peter C. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
