On September 11, 2012 at 2:28 PM Sebastian Juenemann <jueneman@xxxxxxxxxxxxxxxxxxxxxxxx> wrote: > i wanna give some information on that topic too since i've also already > processed PGM TS3.0 data. LifeTech already has altered the SFF output in > such way that its not possible to extract raw sequencing data from the > files, i.e. the quailty clipping points in the sff header are not used > anymore to label 5' adaptor/quality trim points. Ion devs are are aware that they broke something. If you want to crank up the heat up a notch, just write them and ask (nicely!) to fix SFF output until something better comes along :-) B.