From: Peter Cock<p.j.a.cock@xxxxxxxxxxxxxx> > My guess is Bastien used an offset of 59 to give old Solexa > scores shifted to make them start at zero. Nope, Bastien had scaling routines which translated the old Solexa scores to Phred scores not by simple shifting, but according to a formula which James (Bonfield) once published. > Or this is a bug - Bastien did > say he hadn't tested this for a while. Bug. I used those routines in the early day when we got data as FASTA + qual files. Never tested with FASTQ as when I got the first Illumina data in FASTQ, they were already FASTQ-64. B. -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html