To me it seems obvious that if you are running your SOLiD, you want to do so such that the maximum number of reads result. Obviously not at the expense of lower data quality, etc. But just as a general principle: increased numbers of reads for the same run chemistry costs == good.
Under v3+ we had great difficulty achieving the 500 million usable beads per slide metric until it was finally revealed to us that 500 million/slide was pushing the v3+ deposition method to the extreme. We had to deposit well over 1 billion beads to reach 500 million beads per slide.
So now we are nearing the time when we will be doing our first v4 depositions. New deposition procedure, said to give higher deposition efficiency but similar issue: we want to deposit the number of beads that will result in 700 million beads/slide, but not more. (Well, 710M or 720M would probably be okay.) The manual is no help at all in this matter and our FAS will only tell us to be conservative. You know, deposit 700 million beads and see what you get.
So, I am sure there are v4 runs that have been started at least. How about we post our real world "number of beads deposited" vs. "number of usable beads" results? This would all be done under the caveat that if you do go substantially over 700 million beads/slide, then you will likely have numerous panels will bead densities too high for the software to process.
That said, what, in your hands, did it take to get to x number of "usable beads" under v4?
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Phillip
Under v3+ we had great difficulty achieving the 500 million usable beads per slide metric until it was finally revealed to us that 500 million/slide was pushing the v3+ deposition method to the extreme. We had to deposit well over 1 billion beads to reach 500 million beads per slide.
So now we are nearing the time when we will be doing our first v4 depositions. New deposition procedure, said to give higher deposition efficiency but similar issue: we want to deposit the number of beads that will result in 700 million beads/slide, but not more. (Well, 710M or 720M would probably be okay.) The manual is no help at all in this matter and our FAS will only tell us to be conservative. You know, deposit 700 million beads and see what you get.
So, I am sure there are v4 runs that have been started at least. How about we post our real world "number of beads deposited" vs. "number of usable beads" results? This would all be done under the caveat that if you do go substantially over 700 million beads/slide, then you will likely have numerous panels will bead densities too high for the software to process.
That said, what, in your hands, did it take to get to x number of "usable beads" under v4?
--
Phillip
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