On Thu, Oct 6, 2011 at 7:16 AM, Peter Menzel <ptr@xxxxxxxxxx> wrote: > On 6 October 2011 00:12, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: >> Damn. Never tested Illumina 1.0 format in FSTQ, too old. My bad. >> >> Your only option at the moment: convert the FASTQ to standard FASTQ. I think >> one can use the FASTX toolkit for that, but I forgot how. >> > > Ah ok, why does mira guess an offset of 59, which seems to be the > problem? I know there are 3 different Solexa formats, but either they > use ASCII offset of 33 or 64? > > best, Peter While PHRED scores are from 0 upwards, the old Solexa scores could go down to -5. So, with an old Solexa FASTQ, while the ASCII offset was 64, the lowest score had ASCII 64 - 5 = 59. My guess is Bastien used an offset of 59 to give old Solexa scores shifted to make them start at zero. Not ideal, because that will inflate the reasonable/good scores which are almost equal to the PHRED scores. Or this is a bug - Bastien did say he hadn't tested this for a while. However, the old Solexa FASTQ format is practically dead. You might as well convert it to Sanger FASTQ (which will rescale from Solexa -5 to about 40 to PHRED from 0 to about 40). See: http://dx.doi.org/10.1093/nar/gkp1137 Peter -- 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