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Old 01-05-2013, 11:30 PM   #1
lethalfang
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Location: San Francisco, CA

Join Date: Aug 2011
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Default How many samples can I run on an AmpliSeq custom panel order?

We're thinking about MISeq and Ion Torrent, and I'm trying to figure out the custom panels for these 2 platforms.
I tried the AmpliSeq design, and it tells me it's good for a total of ~9000 library construction reactions.


Now here is a stupid question. How many samples can I run with 9000 library constructions? Let's say the target region is about 100 kbp, and I am sequencing an average of 100x coverage. How do I calculate for the number of samples can I sequence with "9000 reactions?"

Thanks in advance.
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Old 01-15-2013, 07:12 AM   #2
anupparikh
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Location: houston, tx

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Default 9000 reactions = 9000 samples

the number of reactions is equal to the number of samples. So you'll be able to amplify and sequence 9000 DNA samples on the PGM.

The multiplex pool contains all the primers needed to amplify anywhere between 1Kb and 1Mb of targeted region, and enough primers are provided to process 9000 DNA samples.

The depth of coverage you're targeting depending on which chip you use for sequencing. Consider the size of your panel, the depth of coverage you need and the throughput of the chip.

Lets say you're targeting 10Kb and need minimum 100x coverage. For AmpliSeq you want to shoot average coverage 5x the minimum coverage. So in this case you'd want to shoot for 10Kb * 500 = 5Mb of total sequencing.

You could use a 314 chip or barcode many samples on a 316/318 chips.
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