Ask your FAS's about the super wash protocol for NextSeqs, it is not part of the normal maintenance and I haven't seen much written on it yet. But it worked wonders on our NextSeq when we were having problems with PF and low Q30
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That's interesting -- do you have any before/after specs?
We noticed a huge jump in cluster densities after the 1.3 update, but the PF and Q30 scores weren't looking so hot. Do you know what the wash protocol entails? -
sorry for the late response, I used to get emails when someone answered the post. I don't have specific before and after because the several runs before the super wash were abysmal, since the wash (and since doing it again after our PFs started to slip) we expect to get > 80% PF at the 250K/mm2 with > 80 Q30
The protocol is a little complicated because you have to manually edit a config file and do a series of longish (90') washes with decreasing concentrations of bleach. We do 1.2% then 0.12% then two tween washes--takes all day. If your FAS can't help I can write out our protocolComment
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