Covaris parameters to obtain 300~600bp fragments?
I'm preparing a special Solexa library where I ideally don't want any fragment sizes below 250 bp and the people who sequence it for us don't want the fragment sizes too high so we kind of settle for about 300-600 bp (ideally concentrating on 3-400 bp). My starting material is 1-2 ug of DNA around 60kb in size. I tried the settings recommended by Covaris (10%, 4, 200, 120s) but got too many fragments falling below 250 bp, whereas lowering the settings result in two distinct clusters, one around 2-300 bp and one around 5-600 bp. Has anyone a better set of parameters to recommend? 