Good Beads / Best Beads

[paolo.kunder]

We are running a WT Paired End analysis on SOLiD 5500XL. We noticed that the percent of Fraction of Good/Best Beads drops dramatically after each cycle (from 80% to ~ 50%). It should be normal but I would like to know the optimal range for a good run.
Any suggestions??
Attached the box plot of one lane.
Thanks

[jayalakshmi]

We have also done a WT run and are experiencing the same case (starts from around 70 and drops till 30%). I have attached the attached the box plots for both the F5 and the F3 tag. Also when viewing the run in real time the height of the bars decreases with each ligation. Any suggestions ??

Thanks
Jaya

[JackQuist]

The paired end chemistry requires a ligation step which is not as efficient. It's normal to see F5 dropping off quicker than F3. This is/was the cause of many complaints from Solid/5500 users. Life Tech released a number of technical "fixes" to improve the situation but fundamentally F5 never going to be as good as F3.
My take is both these plots are normal performance for the instrument/chemistry.