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Old 03-09-2011, 10:02 AM   #1
Dr. Hybe
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Default Maximum cluster density for a GA and Hiseq flowcell that still produces good result

Just curious!? At what point does the number of clusters max out the ability of the machine to read it well (from first base report) - on both a HiSeq or GA flowcell? Thanks
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Old 03-09-2011, 12:05 PM   #2
kthai
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For the HiSeq, I have gotten great results when I aim for the 700,000 K/mm^2 cluster density off of the first base report (usually about 90-120 million reads pass filter). I have had some luck with shooting as high as 1,000,000 K/mm^2, but it's hit or miss and I wouldn't recommend it.

For the GAIIx, I usually aim for 350,000 clusters/mm^2 off of the first base report and about 35-40 million reads pass filter.

Hope this helps!
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Old 03-31-2011, 05:04 AM   #3
Zuuhl
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Quote:
Originally Posted by kthai View Post
For the HiSeq, I have gotten great results when I aim for the 700,000 K/mm^2 cluster density off of the first base report (usually about 90-120 million reads pass filter). I have had some luck with shooting as high as 1,000,000 K/mm^2, but it's hit or miss and I wouldn't recommend it.

For the GAIIx, I usually aim for 350,000 clusters/mm^2 off of the first base report and about 35-40 million reads pass filter.

Hope this helps!
About the GAIIx, I assume it is 350,000 clusters/tile?
Out of curiosity, what concentration are you loading on the GAIIx?

Best Regards.
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Old 03-31-2011, 06:37 AM   #4
kthai
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We typically load at 8pM, but this loading concentration may change depending on how multiplexed each lane is.

Also, it is important to note that this "8pM" loading concentration may vary for each lab depending on the choice of QC methods.
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