hmm, this is the "native" bcl to fastq conversion output after demultiplexing with Illumina's CASAVA. I am "sequencing provider"; I usually fix the header to end up with something like /1,/2 etc. Sven 2011/10/14 Bastien Chevreux <bach@xxxxxxxxxxxx> > ** > > On Friday 14 October 2011 19:29:38 Sven Klages wrote: > > > Is that a change in 1.8.1? In 1.8.0 though the (new) fastq header looks > > > like this: > > > > > > @HW-ST535:67:81C9WABXX:8:1101:2452:2200 1:N:0:ATCACG > > > > > > (note the whitespace just prior to the read number). > > > > > > 1=first read, 2=index read, 3=second read in a pe run with index. But > this > > > is the same as in 1.7. > > > Did I get something wrong here?? > > > Seems like things are a bit unclear atm, maybe also depending on the > sequencing provider. > > > B. >